void CustomIntegrator::initialize(ContextImpl& contextRef) {
if (owner != NULL && &contextRef.getOwner() != owner)
throw OpenMMException("This Integrator is already bound to a context");
vector<std::string> variableList;
set<std::string> variableSet;
variableList.insert(variableList.end(), globalNames.begin(), globalNames.end());
variableList.insert(variableList.end(), perDofNames.begin(), perDofNames.end());
for (int i = 0; i < (int) variableList.size(); i++) {
string& name = variableList[i];
if (variableSet.find(name) != variableSet.end())
throw OpenMMException("The Integrator defines two variables with the same name: "+name);
variableSet.insert(name);
if (contextRef.getParameters().find(name) != contextRef.getParameters().end())
throw OpenMMException("The Integrator defines a variable with the same name as a Context parameter: "+name);
}
set<std::string> globalTargets;
globalTargets.insert(globalNames.begin(), globalNames.end());
globalTargets.insert("dt");
for (map<string, double>::const_iterator iter = contextRef.getParameters().begin(); iter != contextRef.getParameters().end(); ++iter)
globalTargets.insert(iter->first);
for (int i = 0; i < computations.size(); i++) {
if (computations[i].type == ComputeGlobal && globalTargets.find(computations[i].variable) == globalTargets.end())
throw OpenMMException("Unknown global variable: "+computations[i].variable);
}
context = &contextRef;
owner = &contextRef.getOwner();
kernel = context->getPlatform().createKernel(IntegrateCustomStepKernel::Name(), contextRef);
kernel.getAs<IntegrateCustomStepKernel>().initialize(contextRef.getSystem(), *this);
kernel.getAs<IntegrateCustomStepKernel>().setGlobalVariables(contextRef, globalValues);
for (int i = 0; i < (int) perDofValues.size(); i++) {
if (perDofValues[i].size() == 1)
perDofValues[i].resize(context->getSystem().getNumParticles(), perDofValues[i][0]);
kernel.getAs<IntegrateCustomStepKernel>().setPerDofVariable(contextRef, i, perDofValues[i]);
}
}
ExpressionTreeNode ReferenceCustomDynamics::replaceDerivFunctions(const ExpressionTreeNode& node, ContextImpl& context) {
const Operation& op = node.getOperation();
if (op.getId() == Operation::CUSTOM && op.getName() == "deriv") {
string param = node.getChildren()[1].getOperation().getName();
if (context.getParameters().find(param) == context.getParameters().end())
throw OpenMMException("The second argument to deriv() must be a context parameter");
return ExpressionTreeNode(new Operation::Custom("deriv", new DerivFunction(energyParamDerivs, param)));
}
else {
vector<ExpressionTreeNode> children;
for (int i = 0; i < (int) node.getChildren().size(); i++)
children.push_back(replaceDerivFunctions(node.getChildren()[i], context));
return ExpressionTreeNode(op.clone(), children);
}
}
void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses,
map<string, RealOpenMM>& globals, vector<vector<RealVec> >& perDof, bool& forcesAreValid, RealOpenMM tolerance) {
if (invalidatesForces.size() == 0)
initialize(context, masses, globals);
int numSteps = stepType.size();
globals.insert(context.getParameters().begin(), context.getParameters().end());
for (map<string, RealOpenMM>::const_iterator iter = globals.begin(); iter != globals.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
oldPos = atomCoordinates;
// Loop over steps and execute them.
for (int step = 0; step < numSteps; ) {
if ((needsForces[step] || needsEnergy[step]) && (!forcesAreValid || context.getLastForceGroups() != forceGroupFlags[step])) {
// Recompute forces and/or energy.
bool computeForce = needsForces[step] || computeBothForceAndEnergy[step];
bool computeEnergy = needsEnergy[step] || computeBothForceAndEnergy[step];
recordChangedParameters(context, globals);
RealOpenMM e = context.calcForcesAndEnergy(computeForce, computeEnergy, forceGroupFlags[step]);
if (computeEnergy) {
energy = e;
context.getEnergyParameterDerivatives(energyParamDerivs);
}
forcesAreValid = true;
}
// Execute the step.
int nextStep = step+1;
switch (stepType[step]) {
case CustomIntegrator::ComputeGlobal: {
uniform = SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber();
gaussian = SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
RealOpenMM result = stepExpressions[step][0].evaluate();
globals[stepVariable[step]] = result;
expressionSet.setVariable(stepVariableIndex[step], result);
break;
}
case CustomIntegrator::ComputePerDof: {
vector<RealVec>* results = NULL;
if (stepVariableIndex[step] == xIndex)
results = &atomCoordinates;
else if (stepVariableIndex[step] == vIndex)
results = &velocities;
else {
for (int j = 0; j < integrator.getNumPerDofVariables(); j++)
if (stepVariableIndex[step] == perDofVariableIndex[j])
results = &perDof[j];
}
if (results == NULL)
throw OpenMMException("Illegal per-DOF output variable: "+stepVariable[step]);
computePerDof(numberOfAtoms, *results, atomCoordinates, velocities, forces, masses, perDof, stepExpressions[step][0]);
break;
}
case CustomIntegrator::ComputeSum: {
computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, forces, masses, perDof, stepExpressions[step][0]);
RealOpenMM sum = 0.0;
for (int j = 0; j < numberOfAtoms; j++)
if (masses[j] != 0.0)
sum += sumBuffer[j][0]+sumBuffer[j][1]+sumBuffer[j][2];
globals[stepVariable[step]] = sum;
expressionSet.setVariable(stepVariableIndex[step], sum);
break;
}
case CustomIntegrator::ConstrainPositions: {
getReferenceConstraintAlgorithm()->apply(oldPos, atomCoordinates, inverseMasses, tolerance);
oldPos = atomCoordinates;
break;
}
case CustomIntegrator::ConstrainVelocities: {
getReferenceConstraintAlgorithm()->applyToVelocities(oldPos, velocities, inverseMasses, tolerance);
break;
}
case CustomIntegrator::UpdateContextState: {
recordChangedParameters(context, globals);
context.updateContextState();
globals.insert(context.getParameters().begin(), context.getParameters().end());
for (map<string, RealOpenMM>::const_iterator iter = globals.begin(); iter != globals.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
break;
}
case CustomIntegrator::IfBlockStart: {
if (!evaluateCondition(step))
nextStep = blockEnd[step]+1;
break;
}
case CustomIntegrator::WhileBlockStart: {
if (!evaluateCondition(step))
nextStep = blockEnd[step]+1;
break;
}
case CustomIntegrator::BlockEnd: {
if (blockEnd[step] != -1)
nextStep = blockEnd[step]; // Return to the start of a while block.
break;
}
}
if (invalidatesForces[step])
forcesAreValid = false;
step = nextStep;
}
ReferenceVirtualSites::computePositions(context.getSystem(), atomCoordinates);
incrementTimeStep();
recordChangedParameters(context, globals);
}
void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses,
map<string, RealOpenMM>& globals, vector<vector<RealVec> >& perDof, bool& forcesAreValid, RealOpenMM tolerance) {
int numSteps = stepType.size();
globals.insert(context.getParameters().begin(), context.getParameters().end());
oldPos = atomCoordinates;
if (invalidatesForces.size() == 0) {
// Some initialization can't be done in the constructor, since we need a ContextImpl from which to get the list of
// Context parameters. Instead, we do it the first time this method is called.
vector<int> forceGroup;
vector<vector<Lepton::ParsedExpression> > expressions;
CustomIntegratorUtilities::analyzeComputations(context, integrator, expressions, comparisons, blockEnd, invalidatesForces, needsForces, needsEnergy, computeBothForceAndEnergy, forceGroup);
stepExpressions.resize(expressions.size());
for (int i = 0; i < numSteps; i++) {
for (int j = 0; j < (int) expressions[i].size(); j++)
stepExpressions[i].push_back(expressions[i][j].createProgram());
if (stepType[i] == CustomIntegrator::BeginWhileBlock)
blockEnd[blockEnd[i]] = i; // Record where to branch back to.
}
// Record the variable names and flags for the force and energy in each step.
forceGroupFlags.resize(numSteps, -1);
forceName.resize(numSteps, "f");
energyName.resize(numSteps, "energy");
vector<string> forceGroupName;
vector<string> energyGroupName;
for (int i = 0; i < 32; i++) {
stringstream fname;
fname << "f" << i;
forceGroupName.push_back(fname.str());
stringstream ename;
ename << "energy" << i;
energyGroupName.push_back(ename.str());
}
for (int i = 0; i < numSteps; i++) {
if (needsForces[i] && forceGroup[i] > -1)
forceName[i] = forceGroupName[forceGroup[i]];
if (needsEnergy[i] && forceGroup[i] > -1)
energyName[i] = energyGroupName[forceGroup[i]];
if (forceGroup[i] > -1)
forceGroupFlags[i] = 1<<forceGroup[i];
}
// Build the list of inverse masses.
inverseMasses.resize(numberOfAtoms);
for (int i = 0; i < numberOfAtoms; i++) {
if (masses[i] == 0.0)
inverseMasses[i] = 0.0;
else
inverseMasses[i] = 1.0/masses[i];
}
}
// Loop over steps and execute them.
for (int step = 0; step < numSteps; ) {
if ((needsForces[step] || needsEnergy[step]) && (!forcesAreValid || context.getLastForceGroups() != forceGroupFlags[step])) {
// Recompute forces and/or energy.
bool computeForce = needsForces[step] || computeBothForceAndEnergy[step];
bool computeEnergy = needsEnergy[step] || computeBothForceAndEnergy[step];
recordChangedParameters(context, globals);
RealOpenMM e = context.calcForcesAndEnergy(computeForce, computeEnergy, forceGroupFlags[step]);
if (computeEnergy)
energy = e;
forcesAreValid = true;
}
globals[energyName[step]] = energy;
// Execute the step.
int nextStep = step+1;
switch (stepType[step]) {
case CustomIntegrator::ComputeGlobal: {
map<string, RealOpenMM> variables = globals;
variables["uniform"] = SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber();
variables["gaussian"] = SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
globals[stepVariable[step]] = stepExpressions[step][0].evaluate(variables);
break;
}
case CustomIntegrator::ComputePerDof: {
vector<RealVec>* results = NULL;
if (stepVariable[step] == "x")
results = &atomCoordinates;
else if (stepVariable[step] == "v")
results = &velocities;
else {
for (int j = 0; j < integrator.getNumPerDofVariables(); j++)
if (stepVariable[step] == integrator.getPerDofVariableName(j))
results = &perDof[j];
}
if (results == NULL)
throw OpenMMException("Illegal per-DOF output variable: "+stepVariable[step]);
computePerDof(numberOfAtoms, *results, atomCoordinates, velocities, forces, masses, globals, perDof, stepExpressions[step][0], forceName[step]);
break;
}
case CustomIntegrator::ComputeSum: {
computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, forces, masses, globals, perDof, stepExpressions[step][0], forceName[step]);
RealOpenMM sum = 0.0;
for (int j = 0; j < numberOfAtoms; j++)
if (masses[j] != 0.0)
sum += sumBuffer[j][0]+sumBuffer[j][1]+sumBuffer[j][2];
globals[stepVariable[step]] = sum;
break;
}
case CustomIntegrator::ConstrainPositions: {
getReferenceConstraintAlgorithm()->apply(oldPos, atomCoordinates, inverseMasses, tolerance);
oldPos = atomCoordinates;
break;
}
case CustomIntegrator::ConstrainVelocities: {
getReferenceConstraintAlgorithm()->applyToVelocities(oldPos, velocities, inverseMasses, tolerance);
break;
}
case CustomIntegrator::UpdateContextState: {
recordChangedParameters(context, globals);
context.updateContextState();
globals.insert(context.getParameters().begin(), context.getParameters().end());
break;
}
case CustomIntegrator::BeginIfBlock: {
if (!evaluateCondition(step, globals))
nextStep = blockEnd[step]+1;
break;
}
case CustomIntegrator::BeginWhileBlock: {
if (!evaluateCondition(step, globals))
nextStep = blockEnd[step]+1;
break;
}
case CustomIntegrator::EndBlock: {
if (blockEnd[step] != -1)
nextStep = blockEnd[step]; // Return to the start of a while block.
break;
}
}
if (invalidatesForces[step])
forcesAreValid = false;
step = nextStep;
}
ReferenceVirtualSites::computePositions(context.getSystem(), atomCoordinates);
incrementTimeStep();
recordChangedParameters(context, globals);
}
void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses,
map<string, RealOpenMM>& globals, vector<vector<RealVec> >& perDof, bool& forcesAreValid, RealOpenMM tolerance){
int numSteps = stepType.size();
globals.insert(context.getParameters().begin(), context.getParameters().end());
oldPos = atomCoordinates;
if (invalidatesForces.size() == 0) {
// The first time this is called, work out when to recompute forces and energy. First build a
// list of every step that invalidates the forces.
invalidatesForces.resize(numSteps, false);
needsForces.resize(numSteps, false);
needsEnergy.resize(numSteps, false);
forceGroup.resize(numSteps, -2);
forceName.resize(numSteps, "f");
energyName.resize(numSteps, "energy");
set<string> affectsForce;
affectsForce.insert("x");
for (vector<ForceImpl*>::const_iterator iter = context.getForceImpls().begin(); iter != context.getForceImpls().end(); ++iter) {
const map<string, double> params = (*iter)->getDefaultParameters();
for (map<string, double>::const_iterator param = params.begin(); param != params.end(); ++param)
affectsForce.insert(param->first);
}
for (int i = 0; i < numSteps; i++)
invalidatesForces[i] = (stepType[i] == CustomIntegrator::ConstrainPositions || affectsForce.find(stepVariable[i]) != affectsForce.end());
// Make a list of which steps require valid forces or energy to be known.
vector<string> forceGroupName;
vector<string> energyGroupName;
for (int i = 0; i < 32; i++) {
stringstream fname;
fname << "f" << i;
forceGroupName.push_back(fname.str());
stringstream ename;
ename << "energy" << i;
energyGroupName.push_back(ename.str());
}
for (int i = 0; i < numSteps; i++) {
if (stepType[i] == CustomIntegrator::ComputeGlobal || stepType[i] == CustomIntegrator::ComputePerDof || stepType[i] == CustomIntegrator::ComputeSum) {
for (int j = 0; j < stepExpression[i].getNumOperations(); j++) {
const Lepton::Operation& op = stepExpression[i].getOperation(j);
if (op.getId() == Lepton::Operation::VARIABLE) {
if (op.getName() == "energy") {
if (forceGroup[i] != -2)
throw OpenMMException("A single computation step cannot depend on multiple force groups");
needsEnergy[i] = true;
forceGroup[i] = -1;
}
else if (op.getName().substr(0, 6) == "energy") {
for (int k = 0; k < (int) energyGroupName.size(); k++)
if (op.getName() == energyGroupName[k]) {
if (forceGroup[i] != -2)
throw OpenMMException("A single computation step cannot depend on multiple force groups");
needsForces[i] = true;
forceGroup[i] = 1<<k;
energyName[i] = energyGroupName[k];
break;
}
}
else if (op.getName() == "f") {
if (forceGroup[i] != -2)
throw OpenMMException("A single computation step cannot depend on multiple force groups");
needsForces[i] = true;
forceGroup[i] = -1;
}
else if (op.getName()[0] == 'f') {
for (int k = 0; k < (int) forceGroupName.size(); k++)
if (op.getName() == forceGroupName[k]) {
if (forceGroup[i] != -2)
throw OpenMMException("A single computation step cannot depend on multiple force groups");
needsForces[i] = true;
forceGroup[i] = 1<<k;
forceName[i] = forceGroupName[k];
break;
}
}
}
}
}
}
// Build the list of inverse masses.
inverseMasses.resize(numberOfAtoms);
for (int i = 0; i < numberOfAtoms; i++) {
if (masses[i] == 0.0)
inverseMasses[i] = 0.0;
else
inverseMasses[i] = 1.0/masses[i];
}
}
// Loop over steps and execute them.
for (int i = 0; i < numSteps; i++) {
if ((needsForces[i] || needsEnergy[i]) && (!forcesAreValid || context.getLastForceGroups() != forceGroup[i])) {
// Recompute forces and or energy. Figure out what is actually needed
// between now and the next time they get invalidated again.
bool computeForce = false, computeEnergy = false;
for (int j = i; ; j++) {
if (needsForces[j])
computeForce = true;
if (needsEnergy[j])
computeEnergy = true;
if (invalidatesForces[j])
break;
if (j == numSteps-1)
j = -1;
if (j == i-1)
break;
}
recordChangedParameters(context, globals);
RealOpenMM e = context.calcForcesAndEnergy(computeForce, computeEnergy, forceGroup[i]);
if (computeEnergy)
energy = e;
forcesAreValid = true;
}
globals[energyName[i]] = energy;
// Execute the step.
switch (stepType[i]) {
case CustomIntegrator::ComputeGlobal: {
map<string, RealOpenMM> variables = globals;
variables["uniform"] = SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber();
variables["gaussian"] = SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
globals[stepVariable[i]] = stepExpression[i].evaluate(variables);
break;
}
case CustomIntegrator::ComputePerDof: {
vector<RealVec>* results = NULL;
if (stepVariable[i] == "x")
results = &atomCoordinates;
else if (stepVariable[i] == "v")
results = &velocities;
else {
for (int j = 0; j < integrator.getNumPerDofVariables(); j++)
if (stepVariable[i] == integrator.getPerDofVariableName(j))
results = &perDof[j];
}
if (results == NULL)
throw OpenMMException("Illegal per-DOF output variable: "+stepVariable[i]);
computePerDof(numberOfAtoms, *results, atomCoordinates, velocities, forces, masses, globals, perDof, stepExpression[i], forceName[i]);
break;
}
case CustomIntegrator::ComputeSum: {
computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, forces, masses, globals, perDof, stepExpression[i], forceName[i]);
RealOpenMM sum = 0.0;
for (int j = 0; j < numberOfAtoms; j++)
if (masses[j] != 0.0)
sum += sumBuffer[j][0]+sumBuffer[j][1]+sumBuffer[j][2];
globals[stepVariable[i]] = sum;
break;
}
case CustomIntegrator::ConstrainPositions: {
getReferenceConstraintAlgorithm()->apply(oldPos, atomCoordinates, inverseMasses, tolerance);
oldPos = atomCoordinates;
break;
}
case CustomIntegrator::ConstrainVelocities: {
getReferenceConstraintAlgorithm()->applyToVelocities(oldPos, velocities, inverseMasses, tolerance);
break;
}
case CustomIntegrator::UpdateContextState: {
recordChangedParameters(context, globals);
context.updateContextState();
globals.insert(context.getParameters().begin(), context.getParameters().end());
}
}
if (invalidatesForces[i])
forcesAreValid = false;
}
ReferenceVirtualSites::computePositions(context.getSystem(), atomCoordinates);
incrementTimeStep();
recordChangedParameters(context, globals);
}