ReferenceCustomDynamics::ReferenceCustomDynamics(int numberOfAtoms, const CustomIntegrator& integrator) :
ReferenceDynamics(numberOfAtoms, integrator.getStepSize(), 0.0), integrator(integrator) {
sumBuffer.resize(numberOfAtoms);
oldPos.resize(numberOfAtoms);
stepType.resize(integrator.getNumComputations());
stepVariable.resize(integrator.getNumComputations());
for (int i = 0; i < integrator.getNumComputations(); i++) {
string expression;
integrator.getComputationStep(i, stepType[i], stepVariable[i], expression);
}
}
ReferenceCustomDynamics::ReferenceCustomDynamics(int numberOfAtoms, const CustomIntegrator& integrator) :
ReferenceDynamics(numberOfAtoms, integrator.getStepSize(), 0.0), integrator(integrator) {
sumBuffer.resize(numberOfAtoms);
oldPos.resize(numberOfAtoms);
stepType.resize(integrator.getNumComputations());
stepVariable.resize(integrator.getNumComputations());
for (int i = 0; i < integrator.getNumComputations(); i++) {
string expression;
integrator.getComputationStep(i, stepType[i], stepVariable[i], expression);
}
kineticEnergyExpression = Lepton::Parser::parse(integrator.getKineticEnergyExpression()).optimize().createProgram();
kineticEnergyNeedsForce = false;
for (int i = 0; i < kineticEnergyExpression.getNumOperations(); i++) {
const Lepton::Operation& op = kineticEnergyExpression.getOperation(i);
if (op.getId() == Lepton::Operation::VARIABLE && op.getName() == "f")
kineticEnergyNeedsForce = true;
}
}
void CustomIntegratorUtilities::analyzeComputations(const ContextImpl& context, const CustomIntegrator& integrator, vector<vector<Lepton::ParsedExpression> >& expressions,
vector<Comparison>& comparisons, vector<int>& blockEnd, vector<bool>& invalidatesForces, vector<bool>& needsForces, vector<bool>& needsEnergy,
vector<bool>& computeBoth, vector<int>& forceGroup) {
int numSteps = integrator.getNumComputations();
expressions.resize(numSteps);
comparisons.resize(numSteps);
invalidatesForces.resize(numSteps, false);
needsForces.resize(numSteps, false);
needsEnergy.resize(numSteps, false);
computeBoth.resize(numSteps, false);
forceGroup.resize(numSteps, -2);
vector<CustomIntegrator::ComputationType> stepType(numSteps);
vector<string> stepVariable(numSteps);
// Parse the expressions.
for (int step = 0; step < numSteps; step++) {
string expression;
integrator.getComputationStep(step, stepType[step], stepVariable[step], expression);
if (stepType[step] == CustomIntegrator::BeginIfBlock || stepType[step] == CustomIntegrator::BeginWhileBlock) {
// This step involves a condition.
string lhs, rhs;
parseCondition(expression, lhs, rhs, comparisons[step]);
expressions[step].push_back(Lepton::Parser::parse(lhs).optimize());
expressions[step].push_back(Lepton::Parser::parse(rhs).optimize());
}
else if (expression.size() > 0)
expressions[step].push_back(Lepton::Parser::parse(expression).optimize());
}
// Identify which steps invalidate the forces.
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 step = 0; step < numSteps; step++) {
for (int expr = 0; expr < expressions[step].size(); expr++) {
if (usesVariable(expressions[step][expr], "f")) {
needsForces[step] = true;
forceGroup[step] = -1;
}
if (usesVariable(expressions[step][expr], "energy")) {
needsEnergy[step] = true;
forceGroup[step] = -1;
}
for (int i = 0; i < 32; i++) {
if (usesVariable(expressions[step][expr], forceGroupName[i])) {
if (forceGroup[step] != -2)
throw OpenMMException("A single computation step cannot depend on multiple force groups");
needsForces[step] = true;
forceGroup[step] = i;
}
if (usesVariable(expressions[step][expr], energyGroupName[i])) {
if (forceGroup[step] != -2)
throw OpenMMException("A single computation step cannot depend on multiple force groups");
needsEnergy[step] = true;
forceGroup[step] = i;
}
}
}
}
for (int step = numSteps-2; step >= 0; step--)
if (forceGroup[step] == -2)
forceGroup[step] = forceGroup[step+1];
// Find the end point of each block.
vector<int> blockStart;
blockEnd.resize(numSteps, -1);
for (int step = 0; step < numSteps; step++) {
if (stepType[step] == CustomIntegrator::BeginIfBlock || stepType[step] == CustomIntegrator::BeginWhileBlock)
blockStart.push_back(step);
else if (stepType[step] == CustomIntegrator::EndBlock) {
if (blockStart.size() == 0) {
stringstream error("CustomIntegrator: Unexpected end of block at computation ");
error << step;
throw OpenMMException(error.str());
}
blockEnd[blockStart.back()] = step;
blockStart.pop_back();
}
}
if (blockStart.size() > 0)
throw OpenMMException("CustomIntegrator: Missing EndBlock");
// If a step requires either forces or energy, and a later step will require the other one, it's most efficient
// to compute both at the same time. Figure out whether we should do that. In principle it's easy: step through
// the sequence of computations and see if the other one is used before the next time they get invalidated.
// Unfortunately, flow control makes this much more complicated, because there are many possible paths to
// consider.
//
// The cost of computing both when we really only needed one is much less than the cost of computing only one,
// then later finding we need to compute the other separately. So we always err on the side of computing both.
// If there is any possible path that would lead to us needing it, go ahead and compute it.
//
// So we need to enumerate all possible paths. For each "if" block, there are two possibilities: execute it
// or don't. For each "while" block there are three possibilities: don't execute it; execute it and then
// continue on; or execute it and then jump back to the beginning. I'm assuming the number of blocks will
// always remain small. Otherwise, this could become very expensive!
vector<int> jumps(numSteps, -1);
vector<int> stepsInPath;
enumeratePaths(0, stepsInPath, jumps, blockEnd, stepType, needsForces, needsEnergy, invalidatesForces, forceGroup, computeBoth);
}
void testSerializeCustomIntegrator() {
CustomIntegrator *intg = new CustomIntegrator(0.002234);
intg->addPerDofVariable("temp",0);
vector<Vec3> initialValues(123);
for(int i = 0; i < 123; i++)
initialValues[i] = Vec3(i+0.1, i+0.2, i+0.3);
intg->setPerDofVariable(0, initialValues);
intg->addPerDofVariable("oldx", 0);
intg->addComputePerDof("v", "v+dt*f/m");
intg->addComputePerDof("oldx", "x");
intg->addComputePerDof("x", "x+dt*v");
intg->addConstrainPositions();
intg->addComputePerDof("v", "(x-oldx)/dt");
intg->addUpdateContextState();
intg->addConstrainVelocities();
intg->addComputeSum("summand", "x*x+v*v");
intg->addPerDofVariable("outf", 0);
intg->addPerDofVariable("outf1", 0);
intg->addPerDofVariable("outf2", 0);
intg->addGlobalVariable("oute", 0);
intg->addGlobalVariable("oute1", 0);
intg->addGlobalVariable("oute2", 0);
intg->addComputePerDof("outf", "f");
intg->addComputePerDof("outf1", "f1");
intg->addComputePerDof("outf2", "f2");
intg->addComputeGlobal("oute", "energy");
intg->addComputeGlobal("oute1", "energy1");
intg->addComputeGlobal("oute2", "energy2");
intg->addUpdateContextState();
intg->addConstrainVelocities();
intg->addComputeSum("summand2", "v*v+f*f");
intg->setConstraintTolerance(1e-5);
intg->setKineticEnergyExpression("m*v1*v1/2; v1=v+0.5*dt*f/m");
stringstream ss;
XmlSerializer::serialize<Integrator>(intg, "CustomIntegrator", ss);
CustomIntegrator *intg2 = dynamic_cast<CustomIntegrator*>(XmlSerializer::deserialize<Integrator>(ss));
ASSERT_EQUAL(intg->getNumGlobalVariables(), intg->getNumGlobalVariables());
for (int i = 0; i < intg->getNumGlobalVariables(); i++) {
ASSERT_EQUAL(intg->getGlobalVariable(i), intg2->getGlobalVariable(i));
ASSERT_EQUAL(intg->getGlobalVariableName(i), intg2->getGlobalVariableName(i));
}
ASSERT_EQUAL(intg->getNumPerDofVariables(), intg2->getNumPerDofVariables());
for(int i = 0; i < intg->getNumPerDofVariables(); i++) {
vector<Vec3> vars1; intg->getPerDofVariable(i, vars1);
vector<Vec3> vars2; intg2->getPerDofVariable(i, vars2);
ASSERT_EQUAL(vars1.size(),vars2.size());
for (int j = 0; j < (int) vars1.size(); j++) {
ASSERT_EQUAL(vars1[j][0], vars2[j][0]);
ASSERT_EQUAL(vars1[j][1], vars2[j][1]);
ASSERT_EQUAL(vars1[j][2], vars2[j][2]);
}
}
ASSERT_EQUAL(intg->getNumComputations(), intg2->getNumComputations());
for(int i=0; i<intg->getNumComputations(); i++) {
CustomIntegrator::ComputationType type1, type2;
string variable1, variable2;
string expression1, expression2;
intg->getComputationStep(i, type1, variable1, expression1);
intg2->getComputationStep(i, type2, variable2, expression2);
ASSERT_EQUAL(type1, type2);
ASSERT_EQUAL(variable1, variable2);
ASSERT_EQUAL(expression1, expression2);
}
ASSERT_EQUAL(intg->getKineticEnergyExpression(), intg2->getKineticEnergyExpression());
ASSERT_EQUAL(intg->getRandomNumberSeed(), intg2->getRandomNumberSeed());
ASSERT_EQUAL(intg->getStepSize(), intg2->getStepSize());
ASSERT_EQUAL(intg->getConstraintTolerance(), intg2->getConstraintTolerance());
delete intg;
delete intg2;
}