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Commit 0a2439ce authored by Rafal P. Wiewiora's avatar Rafal P. Wiewiora
Browse files

Merge branch 'master' of https://github.com/rafwiewiora/openmm

parents c29de611 6ed5bc4e
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Showing with 446 additions and 477 deletions
platforms/cuda/src/kernels/customHbondForce.cu
View file @ 0a2439ce
......@@ -105,8 +105,8 @@ extern "C" __global__ void computeDonorForces(unsigned long long* __restrict__ f
__syncthreads();
if (donorIndex < NUM_DONORS) {
for (int index = 0; index < blockSize; index++) {
#ifdef USE_EXCLUSIONS
int acceptorIndex = acceptorStart+index;
#ifdef USE_EXCLUSIONS
if (acceptorIndex == exclusionIndices.x || acceptorIndex == exclusionIndices.y || acceptorIndex == exclusionIndices.z || acceptorIndex == exclusionIndices.w)
continue;
#endif
......@@ -193,8 +193,8 @@ extern "C" __global__ void computeAcceptorForces(unsigned long long* __restrict_
__syncthreads();
if (acceptorIndex < NUM_ACCEPTORS) {
for (int index = 0; index < blockSize; index++) {
#ifdef USE_EXCLUSIONS
int donorIndex = donorStart+index;
#ifdef USE_EXCLUSIONS
if (donorIndex == exclusionIndices.x || donorIndex == exclusionIndices.y || donorIndex == exclusionIndices.z || donorIndex == exclusionIndices.w)
continue;
#endif
......
platforms/opencl/src/OpenCLBondedUtilities.cpp
View file @ 0a2439ce
......@@ -184,8 +184,7 @@ void OpenCLBondedUtilities::initialize(const System& system) {
// Create the kernels.
for (vector<vector<int> >::const_iterator iter = forceSets.begin(); iter != forceSets.end(); ++iter) {
const vector<int>& set = *iter;
for (auto& set : forceSets) {
int setSize = set.size();
stringstream s;
s<<"#ifdef SUPPORTS_64_BIT_ATOMICS\n";
......
platforms/opencl/src/OpenCLContext.cpp
View file @ 0a2439ce
......@@ -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/OpenCLExpressionUtilities.cpp
View file @ 0a2439ce
......@@ -448,12 +448,12 @@ void OpenCLExpressionUtilities::processExpression(stringstream& out, const Expre
vector<bool> hasAssigned(powers.size(), false);
exponents.push_back((int) fabs(exponent));
names.push_back(name);
for (map<int, const ExpressionTreeNode*>::const_iterator iter = powers.begin(); iter != powers.end(); ++iter) {
if (iter->first != exponent) {
exponents.push_back(iter->first >= 0 ? iter->first : -iter->first);
for (auto& power : powers) {
if (power.first != exponent) {
exponents.push_back(power.first >= 0 ? power.first : -power.first);
string name2 = prefix+context.intToString(temps.size());
names.push_back(name2);
temps.push_back(make_pair(*iter->second, name2));
temps.push_back(make_pair(*power.second, name2));
out << tempType << " " << name2 << " = 0.0f;\n";
}
}
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ 0a2439ce
This diff is collapsed.
platforms/opencl/src/kernels/customHbondForce.cl
View file @ 0a2439ce
......@@ -91,8 +91,8 @@ __kernel void computeDonorForces(__global real4* restrict forceBuffers, __global
barrier(CLK_LOCAL_MEM_FENCE);
if (donorIndex < NUM_DONORS) {
for (int index = 0; index < blockSize; index++) {
#ifdef USE_EXCLUSIONS
int acceptorIndex = acceptorStart+index;
#ifdef USE_EXCLUSIONS
if (acceptorIndex == exclusionIndices.x || acceptorIndex == exclusionIndices.y || acceptorIndex == exclusionIndices.z || acceptorIndex == exclusionIndices.w)
continue;
#endif
......@@ -179,8 +179,8 @@ __kernel void computeAcceptorForces(__global real4* restrict forceBuffers, __glo
barrier(CLK_LOCAL_MEM_FENCE);
if (acceptorIndex < NUM_ACCEPTORS) {
for (int index = 0; index < blockSize; index++) {
#ifdef USE_EXCLUSIONS
int donorIndex = donorStart+index;
#ifdef USE_EXCLUSIONS
if (donorIndex == exclusionIndices.x || donorIndex == exclusionIndices.y || donorIndex == exclusionIndices.z || donorIndex == exclusionIndices.w)
continue;
#endif
......
platforms/reference/src/ReferenceKernels.cpp
View file @ 0a2439ce
......@@ -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.
......
platforms/reference/src/SimTKReference/ReferenceAndersenThermostat.cpp
View file @ 0a2439ce
......@@ -66,13 +66,12 @@ using namespace OpenMM;
double temperature, double collisionFrequency, double stepSize) const {
const double collisionProbability = 1.0f - exp(-collisionFrequency*stepSize);
for (int i = 0; i < (int) atomGroups.size(); ++i) {
for (auto& group : atomGroups) {
if (SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber() < collisionProbability) {
// A collision occurred, so set the velocities to new values chosen from a Boltzmann distribution.
for (int j = 0; j < (int) atomGroups[i].size(); j++) {
int atom = atomGroups[i][j];
for (int atom : group) {
if (atomMasses[atom] != 0) {
const double velocityScale = static_cast<double>(sqrt(BOLTZ*temperature/atomMasses[atom]));
atomVelocities[atom][0] = velocityScale*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
......
platforms/reference/src/SimTKReference/ReferenceCCMAAlgorithm.cpp
View file @ 0a2439ce
......@@ -127,8 +127,8 @@ ReferenceCCMAAlgorithm::ReferenceCCMAAlgorithm(int numberOfAtoms,
// We didn't find one, so look for an angle force field term.
const vector<int>& angleCandidates = atomAngles[atomb];
for (vector<int>::const_iterator iter = angleCandidates.begin(); iter != angleCandidates.end(); iter++) {
const AngleInfo& angle = angles[*iter];
for (int candidate : angleCandidates) {
const AngleInfo& angle = angles[candidate];
if ((angle.atom1 == atoma && angle.atom3 == atomc) || (angle.atom3 == atoma && angle.atom1 == atomc)) {
matrix[j].push_back(pair<int, double>(k, scale*cos(angle.angle)));
break;
......@@ -145,8 +145,7 @@ ReferenceCCMAAlgorithm::ReferenceCCMAAlgorithm(int numberOfAtoms,
vector<double> matrixValue;
for (int i = 0; i < numberOfConstraints; i++) {
matrixRowStart.push_back(matrixValue.size());
for (int j = 0; j < (int) matrix[i].size(); j++) {
pair<int, double> element = matrix[i][j];
for (auto& element : matrix[i]) {
matrixColIndex.push_back(element.first);
matrixValue.push_back(element.second);
}
......@@ -292,10 +291,8 @@ void ReferenceCCMAAlgorithm::applyConstraints(vector<Vec3>& atomCoordinates,
if (_matrix.size() > 0) {
for (int i = 0; i < _numberOfConstraints; i++) {
double sum = 0.0;
for (int j = 0; j < (int) _matrix[i].size(); j++) {
pair<int, double> element = _matrix[i][j];
for (auto& element : _matrix[i])
sum += element.second*constraintDelta[element.first];
}
tempDelta[i] = sum;
}
constraintDelta = tempDelta;
......
platforms/reference/src/SimTKReference/ReferenceCustomAngleIxn.cpp
View file @ 0a2439ce
......@@ -47,10 +47,10 @@ ReferenceCustomAngleIxn::ReferenceCustomAngleIxn(const Lepton::CompiledExpressio
expressionSet.registerExpression(this->energyParamDerivExpressions[i]);
thetaIndex = expressionSet.getVariableIndex("theta");
numParameters = parameterNames.size();
for (int i = 0; i < (int) numParameters; i++)
angleParamIndex.push_back(expressionSet.getVariableIndex(parameterNames[i]));
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
for (auto& param : parameterNames)
angleParamIndex.push_back(expressionSet.getVariableIndex(param));
for (auto& param : globalParameters)
expressionSet.setVariable(expressionSet.getVariableIndex(param.first), param.second);
}
/**---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferenceCustomBondIxn.cpp
View file @ 0a2439ce
......@@ -48,10 +48,10 @@ ReferenceCustomBondIxn::ReferenceCustomBondIxn(const Lepton::CompiledExpression&
expressionSet.registerExpression(this->energyParamDerivExpressions[i]);
rIndex = expressionSet.getVariableIndex("r");
numParameters = parameterNames.size();
for (int i = 0; i < (int) numParameters; i++)
bondParamIndex.push_back(expressionSet.getVariableIndex(parameterNames[i]));
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
for (auto& param : parameterNames)
bondParamIndex.push_back(expressionSet.getVariableIndex(param));
for (auto& param : globalParameters)
expressionSet.setVariable(expressionSet.getVariableIndex(param.first), param.second);
}
/**---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferenceCustomCentroidBondIxn.cpp
View file @ 0a2439ce
......@@ -56,12 +56,12 @@ ReferenceCustomCentroidBondIxn::ReferenceCustomCentroidBondIxn(int numGroupsPerB
positionTerms.push_back(ReferenceCustomCentroidBondIxn::PositionTermInfo(yname.str(), i, 1, energyExpression.differentiate(yname.str()).createCompiledExpression()));
positionTerms.push_back(ReferenceCustomCentroidBondIxn::PositionTermInfo(zname.str(), i, 2, energyExpression.differentiate(zname.str()).createCompiledExpression()));
}
for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter)
distanceTerms.push_back(ReferenceCustomCentroidBondIxn::DistanceTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).createCompiledExpression()));
for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter)
angleTerms.push_back(ReferenceCustomCentroidBondIxn::AngleTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).createCompiledExpression()));
for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter)
dihedralTerms.push_back(ReferenceCustomCentroidBondIxn::DihedralTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).createCompiledExpression()));
for (auto& term : distances)
distanceTerms.push_back(ReferenceCustomCentroidBondIxn::DistanceTermInfo(term.first, term.second, energyExpression.differentiate(term.first).createCompiledExpression()));
for (auto& term : angles)
angleTerms.push_back(ReferenceCustomCentroidBondIxn::AngleTermInfo(term.first, term.second, energyExpression.differentiate(term.first).createCompiledExpression()));
for (auto& term : dihedrals)
dihedralTerms.push_back(ReferenceCustomCentroidBondIxn::DihedralTermInfo(term.first, term.second, energyExpression.differentiate(term.first).createCompiledExpression()));
for (int i = 0; i < positionTerms.size(); i++) {
expressionSet.registerExpression(positionTerms[i].forceExpression);
positionTerms[i].index = expressionSet.getVariableIndex(positionTerms[i].name);
......@@ -108,8 +108,8 @@ void ReferenceCustomCentroidBondIxn::calculatePairIxn(vector<Vec3>& atomCoordina
// Compute the forces on groups.
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
for (auto& param : globalParameters)
expressionSet.setVariable(expressionSet.getVariableIndex(param.first), param.second);
vector<Vec3> groupForces(numGroups);
int numBonds = bondGroups.size();
for (int bond = 0; bond < numBonds; bond++) {
......@@ -131,23 +131,18 @@ void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<Vec3>& gro
// Compute all of the variables the energy can depend on.
const vector<int>& groups = bondGroups[bond];
for (int i = 0; i < (int) positionTerms.size(); i++) {
const PositionTermInfo& term = positionTerms[i];
for (auto& term : positionTerms)
expressionSet.setVariable(term.index, groupCenters[groups[term.group]][term.component]);
}
for (int i = 0; i < (int) distanceTerms.size(); i++) {
const DistanceTermInfo& term = distanceTerms[i];
for (auto& term : distanceTerms) {
computeDelta(groups[term.g1], groups[term.g2], term.delta, groupCenters);
expressionSet.setVariable(term.index, term.delta[ReferenceForce::RIndex]);
}
for (int i = 0; i < (int) angleTerms.size(); i++) {
const AngleTermInfo& term = angleTerms[i];
for (auto& term : angleTerms) {
computeDelta(groups[term.g1], groups[term.g2], term.delta1, groupCenters);
computeDelta(groups[term.g3], groups[term.g2], term.delta2, groupCenters);
expressionSet.setVariable(term.index, computeAngle(term.delta1, term.delta2));
}
for (int i = 0; i < (int) dihedralTerms.size(); i++) {
const DihedralTermInfo& term = dihedralTerms[i];
for (auto& term : dihedralTerms) {
computeDelta(groups[term.g2], groups[term.g1], term.delta1, groupCenters);
computeDelta(groups[term.g2], groups[term.g3], term.delta2, groupCenters);
computeDelta(groups[term.g4], groups[term.g3], term.delta3, groupCenters);
......@@ -158,15 +153,12 @@ void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<Vec3>& gro
// Apply forces based on individual particle coordinates.
for (int i = 0; i < (int) positionTerms.size(); i++) {
const PositionTermInfo& term = positionTerms[i];
for (auto& term : positionTerms)
forces[groups[term.group]][term.component] -= term.forceExpression.evaluate();
}
// Apply forces based on distances.
for (int i = 0; i < (int) distanceTerms.size(); i++) {
const DistanceTermInfo& term = distanceTerms[i];
for (auto& term : distanceTerms) {
double dEdR = term.forceExpression.evaluate()/(term.delta[ReferenceForce::RIndex]);
for (int i = 0; i < 3; i++) {
double force = -dEdR*term.delta[i];
......@@ -177,8 +169,7 @@ void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<Vec3>& gro
// Apply forces based on angles.
for (int i = 0; i < (int) angleTerms.size(); i++) {
const AngleTermInfo& term = angleTerms[i];
for (auto& term : angleTerms) {
double dEdTheta = term.forceExpression.evaluate();
double thetaCross[ReferenceForce::LastDeltaRIndex];
SimTKOpenMMUtilities::crossProductVector3(term.delta1, term.delta2, thetaCross);
......@@ -204,8 +195,7 @@ void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<Vec3>& gro
// Apply forces based on dihedrals.
for (int i = 0; i < (int) dihedralTerms.size(); i++) {
const DihedralTermInfo& term = dihedralTerms[i];
for (auto& term : dihedralTerms) {
double dEdTheta = term.forceExpression.evaluate();
double internalF[4][3];
double forceFactors[4];
......
platforms/reference/src/SimTKReference/ReferenceCustomCompoundBondIxn.cpp
View file @ 0a2439ce
......@@ -61,12 +61,12 @@ ReferenceCustomCompoundBondIxn::ReferenceCustomCompoundBondIxn(int numParticlesP
particleTerms.push_back(ReferenceCustomCompoundBondIxn::ParticleTermInfo(yname.str(), i, 1, energyExpression.differentiate(yname.str()).createCompiledExpression()));
particleTerms.push_back(ReferenceCustomCompoundBondIxn::ParticleTermInfo(zname.str(), i, 2, energyExpression.differentiate(zname.str()).createCompiledExpression()));
}
for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter)
distanceTerms.push_back(ReferenceCustomCompoundBondIxn::DistanceTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).createCompiledExpression()));
for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter)
angleTerms.push_back(ReferenceCustomCompoundBondIxn::AngleTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).createCompiledExpression()));
for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter)
dihedralTerms.push_back(ReferenceCustomCompoundBondIxn::DihedralTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).createCompiledExpression()));
for (auto& term : distances)
distanceTerms.push_back(ReferenceCustomCompoundBondIxn::DistanceTermInfo(term.first, term.second, energyExpression.differentiate(term.first).createCompiledExpression()));
for (auto& term : angles)
angleTerms.push_back(ReferenceCustomCompoundBondIxn::AngleTermInfo(term.first, term.second, energyExpression.differentiate(term.first).createCompiledExpression()));
for (auto& term : dihedrals)
dihedralTerms.push_back(ReferenceCustomCompoundBondIxn::DihedralTermInfo(term.first, term.second, energyExpression.differentiate(term.first).createCompiledExpression()));
for (int i = 0; i < particleTerms.size(); i++) {
expressionSet.registerExpression(particleTerms[i].forceExpression);
particleTerms[i].index = expressionSet.getVariableIndex(particleTerms[i].name);
......@@ -119,8 +119,8 @@ void ReferenceCustomCompoundBondIxn::setPeriodic(OpenMM::Vec3* vectors) {
void ReferenceCustomCompoundBondIxn::calculatePairIxn(vector<Vec3>& atomCoordinates, double** bondParameters,
const map<string, double>& globalParameters, vector<Vec3>& forces,
double* totalEnergy, double* energyParamDerivs) {
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
for (auto& param : globalParameters)
expressionSet.setVariable(expressionSet.getVariableIndex(param.first), param.second);
int numBonds = bondAtoms.size();
for (int bond = 0; bond < numBonds; bond++) {
for (int i = 0; i < numParameters; i++)
......@@ -146,23 +146,18 @@ void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<Vec3>& ato
// Compute all of the variables the energy can depend on.
const vector<int>& atoms = bondAtoms[bond];
for (int i = 0; i < (int) particleTerms.size(); i++) {
const ParticleTermInfo& term = particleTerms[i];
for (auto& term : particleTerms)
expressionSet.setVariable(term.index, atomCoordinates[atoms[term.atom]][term.component]);
}
for (int i = 0; i < (int) distanceTerms.size(); i++) {
const DistanceTermInfo& term = distanceTerms[i];
for (auto& term : distanceTerms) {
computeDelta(atoms[term.p1], atoms[term.p2], term.delta, atomCoordinates);
expressionSet.setVariable(term.index, term.delta[ReferenceForce::RIndex]);
}
for (int i = 0; i < (int) angleTerms.size(); i++) {
const AngleTermInfo& term = angleTerms[i];
for (auto& term : angleTerms) {
computeDelta(atoms[term.p1], atoms[term.p2], term.delta1, atomCoordinates);
computeDelta(atoms[term.p3], atoms[term.p2], term.delta2, atomCoordinates);
expressionSet.setVariable(term.index, computeAngle(term.delta1, term.delta2));
}
for (int i = 0; i < (int) dihedralTerms.size(); i++) {
const DihedralTermInfo& term = dihedralTerms[i];
for (auto& term : dihedralTerms) {
computeDelta(atoms[term.p2], atoms[term.p1], term.delta1, atomCoordinates);
computeDelta(atoms[term.p2], atoms[term.p3], term.delta2, atomCoordinates);
computeDelta(atoms[term.p4], atoms[term.p3], term.delta3, atomCoordinates);
......@@ -173,15 +168,12 @@ void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<Vec3>& ato
// Apply forces based on individual particle coordinates.
for (int i = 0; i < (int) particleTerms.size(); i++) {
const ParticleTermInfo& term = particleTerms[i];
for (auto& term : particleTerms)
forces[atoms[term.atom]][term.component] -= term.forceExpression.evaluate();
}
// Apply forces based on distances.
for (int i = 0; i < (int) distanceTerms.size(); i++) {
const DistanceTermInfo& term = distanceTerms[i];
for (auto& term : distanceTerms) {
double dEdR = term.forceExpression.evaluate()/(term.delta[ReferenceForce::RIndex]);
for (int i = 0; i < 3; i++) {
double force = -dEdR*term.delta[i];
......@@ -192,8 +184,7 @@ void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<Vec3>& ato
// Apply forces based on angles.
for (int i = 0; i < (int) angleTerms.size(); i++) {
const AngleTermInfo& term = angleTerms[i];
for (auto& term : angleTerms) {
double dEdTheta = term.forceExpression.evaluate();
double thetaCross[ReferenceForce::LastDeltaRIndex];
SimTKOpenMMUtilities::crossProductVector3(term.delta1, term.delta2, thetaCross);
......@@ -219,8 +210,7 @@ void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<Vec3>& ato
// Apply forces based on dihedrals.
for (int i = 0; i < (int) dihedralTerms.size(); i++) {
const DihedralTermInfo& term = dihedralTerms[i];
for (auto& term : dihedralTerms) {
double dEdTheta = term.forceExpression.evaluate();
double internalF[4][3];
double forceFactors[4];
......
platforms/reference/src/SimTKReference/ReferenceCustomDynamics.cpp
View file @ 0a2439ce
......@@ -175,8 +175,8 @@ ExpressionTreeNode ReferenceCustomDynamics::replaceDerivFunctions(const Expressi
}
else {
vector<ExpressionTreeNode> children;
for (int i = 0; i < (int) node.getChildren().size(); i++)
children.push_back(replaceDerivFunctions(node.getChildren()[i], context));
for (auto& child : node.getChildren())
children.push_back(replaceDerivFunctions(child, context));
return ExpressionTreeNode(op.clone(), children);
}
}
......@@ -204,8 +204,8 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
initialize(context, masses, globals);
int numSteps = stepType.size();
globals.insert(context.getParameters().begin(), context.getParameters().end());
for (map<string, double>::const_iterator iter = globals.begin(); iter != globals.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
for (auto& global : globals)
expressionSet.setVariable(expressionSet.getVariableIndex(global.first), global.second);
oldPos = atomCoordinates;
// Loop over steps and execute them.
......@@ -276,8 +276,8 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
recordChangedParameters(context, globals);
context.updateContextState();
globals.insert(context.getParameters().begin(), context.getParameters().end());
for (map<string, double>::const_iterator iter = globals.begin(); iter != globals.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
for (auto& global : globals)
expressionSet.setVariable(expressionSet.getVariableIndex(global.first), global.second);
break;
}
case CustomIntegrator::IfBlockStart: {
......@@ -355,10 +355,10 @@ bool ReferenceCustomDynamics::evaluateCondition(int step) {
* Check which context parameters have changed and register them with the context.
*/
void ReferenceCustomDynamics::recordChangedParameters(OpenMM::ContextImpl& context, std::map<std::string, double>& globals) {
for (map<string, double>::const_iterator iter = context.getParameters().begin(); iter != context.getParameters().end(); ++iter) {
string name = iter->first;
for (auto& param : context.getParameters()) {
string name = param.first;
double value = globals[name];
if (value != iter->second)
if (value != param.second)
context.setParameter(name, globals[name]);
}
}
......@@ -385,8 +385,8 @@ double ReferenceCustomDynamics::computeKineticEnergy(OpenMM::ContextImpl& contex
if (invalidatesForces.size() == 0)
initialize(context, masses, globals);
globals.insert(context.getParameters().begin(), context.getParameters().end());
for (map<string, double>::const_iterator iter = globals.begin(); iter != globals.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
for (auto& global : globals)
expressionSet.setVariable(expressionSet.getVariableIndex(global.first), global.second);
if (kineticEnergyNeedsForce) {
energy = context.calcForcesAndEnergy(true, true, -1);
forcesAreValid = true;
......
platforms/reference/src/SimTKReference/ReferenceCustomExternalIxn.cpp
View file @ 0a2439ce
......@@ -57,17 +57,17 @@ ReferenceCustomExternalIxn::ReferenceCustomExternalIxn(const Lepton::CompiledExp
forceZY = ReferenceForce::getVariablePointer(this->forceExpressionZ, "y");
forceZZ = ReferenceForce::getVariablePointer(this->forceExpressionZ, "z");
numParameters = parameterNames.size();
for (int i = 0; i < (int) numParameters; i++) {
energyParams.push_back(ReferenceForce::getVariablePointer(this->energyExpression, parameterNames[i]));
forceXParams.push_back(ReferenceForce::getVariablePointer(this->forceExpressionX, parameterNames[i]));
forceYParams.push_back(ReferenceForce::getVariablePointer(this->forceExpressionY, parameterNames[i]));
forceZParams.push_back(ReferenceForce::getVariablePointer(this->forceExpressionZ, parameterNames[i]));
for (auto& param : parameterNames) {
energyParams.push_back(ReferenceForce::getVariablePointer(this->energyExpression, param));
forceXParams.push_back(ReferenceForce::getVariablePointer(this->forceExpressionX, param));
forceYParams.push_back(ReferenceForce::getVariablePointer(this->forceExpressionY, param));
forceZParams.push_back(ReferenceForce::getVariablePointer(this->forceExpressionZ, param));
}
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter) {
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->energyExpression, iter->first), iter->second);
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->forceExpressionX, iter->first), iter->second);
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->forceExpressionY, iter->first), iter->second);
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->forceExpressionZ, iter->first), iter->second);
for (auto& param : globalParameters) {
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->energyExpression, param.first), param.second);
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->forceExpressionX, param.first), param.second);
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->forceExpressionY, param.first), param.second);
ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->forceExpressionZ, param.first), param.second);
}
}
......
platforms/reference/src/SimTKReference/ReferenceCustomGBIxn.cpp
View file @ 0a2439ce
......@@ -84,19 +84,19 @@ ReferenceCustomGBIxn::ReferenceCustomGBIxn(const vector<Lepton::CompiledExpressi
xIndex = expressionSet.getVariableIndex("x");
yIndex = expressionSet.getVariableIndex("y");
zIndex = expressionSet.getVariableIndex("z");
for (int i = 0; i < (int) parameterNames.size(); i++) {
paramIndex.push_back(expressionSet.getVariableIndex(parameterNames[i]));
for (auto& param : parameterNames) {
paramIndex.push_back(expressionSet.getVariableIndex(param));
for (int j = 1; j < 3; j++) {
stringstream name;
name << parameterNames[i] << j;
name << param << j;
particleParamIndex.push_back(expressionSet.getVariableIndex(name.str()));
}
}
for (int i = 0; i < (int) valueNames.size(); i++) {
valueIndex.push_back(expressionSet.getVariableIndex(valueNames[i]));
for (auto& value : valueNames) {
valueIndex.push_back(expressionSet.getVariableIndex(value));
for (int j = 1; j < 3; j++) {
stringstream name;
name << valueNames[i] << j;
name << value << j;
particleValueIndex.push_back(expressionSet.getVariableIndex(name.str()));
}
}
......@@ -153,8 +153,8 @@ ReferenceCustomGBIxn::~ReferenceCustomGBIxn() {
void ReferenceCustomGBIxn::calculateIxn(int numberOfAtoms, vector<Vec3>& atomCoordinates, double** atomParameters,
const vector<set<int> >& exclusions, map<string, double>& globalParameters, vector<Vec3>& forces,
double* totalEnergy, double* energyParamDerivs) {
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
for (auto& param : globalParameters)
expressionSet.setVariable(expressionSet.getVariableIndex(param.first), param.second);
// Initialize arrays for storing values.
......@@ -225,8 +225,7 @@ void ReferenceCustomGBIxn::calculateParticlePairValue(int index, int numAtoms, v
if (cutoff) {
// Loop over all pairs in the neighbor list.
for (int i = 0; i < (int) neighborList->size(); i++) {
OpenMM::AtomPair pair = (*neighborList)[i];
for (auto& pair : *neighborList) {
if (useExclusions && exclusions[pair.first].find(pair.second) != exclusions[pair.first].end())
continue;
calculateOnePairValue(index, pair.first, pair.second, atomCoordinates, atomParameters);
......@@ -306,8 +305,7 @@ void ReferenceCustomGBIxn::calculateParticlePairEnergyTerm(int index, int numAto
if (cutoff) {
// Loop over all pairs in the neighbor list.
for (int i = 0; i < (int) neighborList->size(); i++) {
OpenMM::AtomPair pair = (*neighborList)[i];
for (auto& pair : *neighborList) {
if (useExclusions && exclusions[pair.first].find(pair.second) != exclusions[pair.first].end())
continue;
calculateOnePairEnergyTerm(index, pair.first, pair.second, atomCoordinates, atomParameters, forces, totalEnergy, energyParamDerivs);
......@@ -377,8 +375,7 @@ void ReferenceCustomGBIxn::calculateChainRuleForces(int numAtoms, vector<Vec3>&
if (cutoff) {
// Loop over all pairs in the neighbor list.
for (int i = 0; i < (int) neighborList->size(); i++) {
OpenMM::AtomPair pair = (*neighborList)[i];
for (auto& pair : *neighborList) {
bool isExcluded = (exclusions[pair.first].find(pair.second) != exclusions[pair.first].end());
calculateOnePairChainRule(pair.first, pair.second, atomCoordinates, atomParameters, forces, isExcluded);
calculateOnePairChainRule(pair.second, pair.first, atomCoordinates, atomParameters, forces, isExcluded);
......
platforms/reference/src/SimTKReference/ReferenceCustomHbondIxn.cpp
View file @ 0a2439ce
......@@ -49,12 +49,12 @@ ReferenceCustomHbondIxn::ReferenceCustomHbondIxn(const vector<vector<int> >& don
const map<string, vector<int> >& distances, const map<string, vector<int> >& angles, const map<string, vector<int> >& dihedrals) :
cutoff(false), periodic(false), donorAtoms(donorAtoms), acceptorAtoms(acceptorAtoms), energyExpression(energyExpression.createProgram()),
donorParamNames(donorParameterNames), acceptorParamNames(acceptorParameterNames) {
for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter)
distanceTerms.push_back(ReferenceCustomHbondIxn::DistanceTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter)
angleTerms.push_back(ReferenceCustomHbondIxn::AngleTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter)
dihedralTerms.push_back(ReferenceCustomHbondIxn::DihedralTermInfo(iter->first, iter->second, energyExpression.differentiate(iter->first).optimize().createProgram()));
for (auto& term : distances)
distanceTerms.push_back(ReferenceCustomHbondIxn::DistanceTermInfo(term.first, term.second, energyExpression.differentiate(term.first).optimize().createProgram()));
for (auto& term : angles)
angleTerms.push_back(ReferenceCustomHbondIxn::AngleTermInfo(term.first, term.second, energyExpression.differentiate(term.first).optimize().createProgram()));
for (auto& term : dihedrals)
dihedralTerms.push_back(ReferenceCustomHbondIxn::DihedralTermInfo(term.first, term.second, energyExpression.differentiate(term.first).optimize().createProgram()));
}
/**---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferenceCustomManyParticleIxn.cpp
View file @ 0a2439ce
......@@ -60,8 +60,8 @@ ReferenceCustomManyParticleIxn::ReferenceCustomManyParticleIxn(const CustomManyP
// 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;
// Differentiate the energy to get expressions for the force.
......@@ -80,12 +80,12 @@ ReferenceCustomManyParticleIxn::ReferenceCustomManyParticleIxn(const CustomManyP
particleParamNames[i].push_back(paramname.str());
}
}
for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter)
distanceTerms.push_back(ReferenceCustomManyParticleIxn::DistanceTermInfo(iter->first, iter->second, energyExpr.differentiate(iter->first).optimize().createProgram()));
for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter)
angleTerms.push_back(ReferenceCustomManyParticleIxn::AngleTermInfo(iter->first, iter->second, energyExpr.differentiate(iter->first).optimize().createProgram()));
for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter)
dihedralTerms.push_back(ReferenceCustomManyParticleIxn::DihedralTermInfo(iter->first, iter->second, energyExpr.differentiate(iter->first).optimize().createProgram()));
for (auto& term : distances)
distanceTerms.push_back(ReferenceCustomManyParticleIxn::DistanceTermInfo(term.first, term.second, energyExpr.differentiate(term.first).optimize().createProgram()));
for (auto& term : angles)
angleTerms.push_back(ReferenceCustomManyParticleIxn::AngleTermInfo(term.first, term.second, energyExpr.differentiate(term.first).optimize().createProgram()));
for (auto& term : dihedrals)
dihedralTerms.push_back(ReferenceCustomManyParticleIxn::DihedralTermInfo(term.first, term.second, energyExpr.differentiate(term.first).optimize().createProgram()));
// Record exclusions.
......@@ -192,23 +192,18 @@ void ReferenceCustomManyParticleIxn::calculateOneIxn(const vector<int>& particle
// Compute all of the variables the energy can depend on.
for (int i = 0; i < (int) particleTerms.size(); i++) {
const ParticleTermInfo& term = particleTerms[i];
for (auto& term : particleTerms)
variables[term.name] = atomCoordinates[permutedParticles[term.atom]][term.component];
}
for (int i = 0; i < (int) distanceTerms.size(); i++) {
const DistanceTermInfo& term = distanceTerms[i];
for (auto& term : distanceTerms) {
computeDelta(permutedParticles[term.p1], permutedParticles[term.p2], term.delta, atomCoordinates);
variables[term.name] = term.delta[ReferenceForce::RIndex];
}
for (int i = 0; i < (int) angleTerms.size(); i++) {
const AngleTermInfo& term = angleTerms[i];
for (auto& term : angleTerms) {
computeDelta(permutedParticles[term.p1], permutedParticles[term.p2], term.delta1, atomCoordinates);
computeDelta(permutedParticles[term.p3], permutedParticles[term.p2], term.delta2, atomCoordinates);
variables[term.name] = computeAngle(term.delta1, term.delta2);
}
for (int i = 0; i < (int) dihedralTerms.size(); i++) {
const DihedralTermInfo& term = dihedralTerms[i];
for (auto& term : dihedralTerms) {
computeDelta(permutedParticles[term.p2], permutedParticles[term.p1], term.delta1, atomCoordinates);
computeDelta(permutedParticles[term.p2], permutedParticles[term.p3], term.delta2, atomCoordinates);
computeDelta(permutedParticles[term.p4], permutedParticles[term.p3], term.delta3, atomCoordinates);
......@@ -219,15 +214,12 @@ void ReferenceCustomManyParticleIxn::calculateOneIxn(const vector<int>& particle
// Apply forces based on individual particle coordinates.
for (int i = 0; i < (int) particleTerms.size(); i++) {
const ParticleTermInfo& term = particleTerms[i];
for (auto& term : particleTerms)
forces[permutedParticles[term.atom]][term.component] -= term.forceExpression.evaluate(variables);
}
// Apply forces based on distances.
for (int i = 0; i < (int) distanceTerms.size(); i++) {
const DistanceTermInfo& term = distanceTerms[i];
for (auto& term : distanceTerms) {
double dEdR = term.forceExpression.evaluate(variables)/(term.delta[ReferenceForce::RIndex]);
for (int i = 0; i < 3; i++) {
double force = -dEdR*term.delta[i];
......@@ -238,8 +230,7 @@ void ReferenceCustomManyParticleIxn::calculateOneIxn(const vector<int>& particle
// Apply forces based on angles.
for (int i = 0; i < (int) angleTerms.size(); i++) {
const AngleTermInfo& term = angleTerms[i];
for (auto& term : angleTerms) {
double dEdTheta = term.forceExpression.evaluate(variables);
double thetaCross[ReferenceForce::LastDeltaRIndex];
SimTKOpenMMUtilities::crossProductVector3(term.delta1, term.delta2, thetaCross);
......@@ -265,8 +256,7 @@ void ReferenceCustomManyParticleIxn::calculateOneIxn(const vector<int>& particle
// Apply forces based on dihedrals.
for (int i = 0; i < (int) dihedralTerms.size(); i++) {
const DihedralTermInfo& term = dihedralTerms[i];
for (auto& term : dihedralTerms) {
double dEdTheta = term.forceExpression.evaluate(variables);
double internalF[4][3];
double forceFactors[4];
......
platforms/reference/src/SimTKReference/ReferenceCustomNonbondedIxn.cpp
View file @ 0a2439ce
......@@ -53,10 +53,10 @@ ReferenceCustomNonbondedIxn::ReferenceCustomNonbondedIxn(const Lepton::CompiledE
for (int i = 0; i < this->energyParamDerivExpressions.size(); i++)
expressionSet.registerExpression(this->energyParamDerivExpressions[i]);
rIndex = expressionSet.getVariableIndex("r");
for (int i = 0; i < (int) paramNames.size(); i++) {
for (auto& param : paramNames) {
for (int j = 1; j < 3; j++) {
stringstream name;
name << paramNames[i] << j;
name << param << j;
particleParamIndex.push_back(expressionSet.getVariableIndex(name.str()));
}
}
......@@ -159,14 +159,14 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn(int numberOfAtoms, vector<Vec
double* fixedParameters, const map<string, double>& globalParameters, vector<Vec3>& forces,
double* energyByAtom, double* totalEnergy, double* energyParamDerivs) {
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
if (interactionGroups.size() > 0) {
for (auto& param : globalParameters)
expressionSet.setVariable(expressionSet.getVariableIndex(param.first), param.second);
if (interactionGroups.size() > 0) {
// The user has specified interaction groups, so compute only the requested interactions.
for (int group = 0; group < (int) interactionGroups.size(); group++) {
const set<int>& set1 = interactionGroups[group].first;
const set<int>& set2 = interactionGroups[group].second;
for (auto& group : interactionGroups) {
const set<int>& set1 = group.first;
const set<int>& set2 = group.second;
for (set<int>::const_iterator atom1 = set1.begin(); atom1 != set1.end(); ++atom1) {
for (set<int>::const_iterator atom2 = set2.begin(); atom2 != set2.end(); ++atom2) {
if (*atom1 == *atom2 || exclusions[*atom1].find(*atom2) != exclusions[*atom1].end())
......@@ -185,8 +185,7 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn(int numberOfAtoms, vector<Vec
else if (cutoff) {
// We are using a cutoff, so get the interactions from the neighbor list.
for (int i = 0; i < (int) neighborList->size(); i++) {
OpenMM::AtomPair pair = (*neighborList)[i];
for (auto& pair : *neighborList) {
for (int j = 0; j < (int) paramNames.size(); j++) {
expressionSet.setVariable(particleParamIndex[j*2], atomParameters[pair.first][j]);
expressionSet.setVariable(particleParamIndex[j*2+1], atomParameters[pair.second][j]);
......
platforms/reference/src/SimTKReference/ReferenceCustomTorsionIxn.cpp
View file @ 0a2439ce
......@@ -47,10 +47,10 @@ ReferenceCustomTorsionIxn::ReferenceCustomTorsionIxn(const Lepton::CompiledExpre
expressionSet.registerExpression(this->energyParamDerivExpressions[i]);
thetaIndex = expressionSet.getVariableIndex("theta");
numParameters = parameterNames.size();
for (int i = 0; i < (int) numParameters; i++)
torsionParamIndex.push_back(expressionSet.getVariableIndex(parameterNames[i]));
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
for (auto& param : parameterNames)
torsionParamIndex.push_back(expressionSet.getVariableIndex(param));
for (auto& param : globalParameters)
expressionSet.setVariable(expressionSet.getVariableIndex(param.first), param.second);
}
/**---------------------------------------------------------------------------------------
......
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