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Commit 44b96f0c authored by peastman's avatar peastman
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Reference implementation of flow control in CustomIntegrator

parent 199feca2
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openmmapi/include/openmm/internal/CustomIntegratorUtilities.h
View file @ 44b96f0c
......@@ -60,16 +60,17 @@ public:
* Analyze the sequence of steps in a CustomIntegrator. For each step:
*
* 1. Parse all expressions involved in the step, and identify the comparison operator (for conditional steps).
* 2. Determine whether the step causes previously computed forces and energies to become invalid.
* 3. Determine whether the step itself needs forces and/or energies.
* 4. Decide whether forces and energies should both be computed at that step (because
* 2. For each conditional block, identify what step marks the end of the block.
* 3. Determine whether the step causes previously computed forces and energies to become invalid.
* 4. Determine whether the step itself needs forces and/or energies.
* 5. Decide whether forces and energies should both be computed at that step (because
* it is more efficient to compute both at once, even if one won't be needed
* until a later step).
* 5. Identify what force group each step needs forces and/or energies for.
* 6. Identify what force group each step needs forces and/or energies for.
*/
static void analyzeComputations(const ContextImpl& context, const CustomIntegrator& integrator, std::vector<std::vector<Lepton::ParsedExpression> >& expressions,
std::vector<Comparison>& comparisons, std::vector<bool>& invalidatesForces, std::vector<bool>& needsForces, std::vector<bool>& needsEnergy,
std::vector<bool>& computeBoth, std::vector<int>& forceGroup);
std::vector<Comparison>& comparisons, std::vector<int>& blockEnd, std::vector<bool>& invalidatesForces, std::vector<bool>& needsForces,
std::vector<bool>& needsEnergy, std::vector<bool>& computeBoth, std::vector<int>& forceGroup);
/**
* Determine whether an expression involves a particular variable.
*/
......
openmmapi/src/CustomIntegratorUtilities.cpp
View file @ 44b96f0c
......@@ -69,7 +69,7 @@ bool CustomIntegratorUtilities::usesVariable(const Lepton::ParsedExpression& exp
}
void CustomIntegratorUtilities::analyzeComputations(const ContextImpl& context, const CustomIntegrator& integrator, vector<vector<Lepton::ParsedExpression> >& expressions,
vector<Comparison>& comparisons, vector<bool>& invalidatesForces, vector<bool>& needsForces, vector<bool>& needsEnergy,
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);
......@@ -138,13 +138,13 @@ void CustomIntegratorUtilities::analyzeComputations(const ContextImpl& context,
if (forceGroup[step] != -2)
throw OpenMMException("A single computation step cannot depend on multiple force groups");
needsForces[step] = true;
forceGroup[step] = 1<<i;
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] = 1<<i;
forceGroup[step] = i;
}
}
}
......@@ -153,7 +153,7 @@ void CustomIntegratorUtilities::analyzeComputations(const ContextImpl& context,
// Find the end point of each block.
vector<int> blockStart;
vector<int> blockEnd(numSteps);
blockEnd.resize(numSteps, -1);
for (int step = 0; step < numSteps; step++) {
if (stepType[step] == CustomIntegrator::BeginIfBlock || stepType[step] == CustomIntegrator::BeginWhileBlock)
blockStart.push_back(step);
......
platforms/reference/include/ReferenceCustomDynamics.h
View file @ 44b96f0c
/* Portions copyright (c) 2011 Stanford University and Simbios.
/* Portions copyright (c) 2011-2015 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -28,6 +28,7 @@
#include "ReferenceDynamics.h"
#include "openmm/CustomIntegrator.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/CustomIntegratorUtilities.h"
#include "lepton/ExpressionProgram.h"
#include <map>
......@@ -44,9 +45,10 @@ private:
std::vector<OpenMM::RealVec> sumBuffer, oldPos;
std::vector<OpenMM::CustomIntegrator::ComputationType> stepType;
std::vector<std::string> stepVariable, forceName, energyName;
std::vector<Lepton::ExpressionProgram> stepExpression;
std::vector<bool> invalidatesForces, needsForces, needsEnergy;
std::vector<int> forceGroup;
std::vector<std::vector<Lepton::ExpressionProgram> > stepExpressions;
std::vector<CustomIntegratorUtilities::Comparison> comparisons;
std::vector<bool> invalidatesForces, needsForces, needsEnergy, computeBothForceAndEnergy;
std::vector<int> forceGroupFlags, blockEnd;
RealOpenMM energy;
Lepton::ExpressionProgram kineticEnergyExpression;
bool kineticEnergyNeedsForce;
......@@ -57,6 +59,8 @@ private:
const Lepton::ExpressionProgram& expression, const std::string& forceName);
void recordChangedParameters(OpenMM::ContextImpl& context, std::map<std::string, RealOpenMM>& globals);
bool evaluateCondition(int step, std::map<std::string, RealOpenMM>& globals);
public:
......
platforms/reference/src/SimTKReference/ReferenceCustomDynamics.cpp
View file @ 44b96f0c
/* Portions copyright (c) 2011-2013 Stanford University and Simbios.
/* Portions copyright (c) 2011-2015 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -52,12 +52,9 @@ ReferenceCustomDynamics::ReferenceCustomDynamics(int numberOfAtoms, const Custom
oldPos.resize(numberOfAtoms);
stepType.resize(integrator.getNumComputations());
stepVariable.resize(integrator.getNumComputations());
stepExpression.resize(integrator.getNumComputations());
for (int i = 0; i < integrator.getNumComputations(); i++) {
string expression;
integrator.getComputationStep(i, stepType[i], stepVariable[i], expression);
if (expression.length() > 0)
stepExpression[i] = Lepton::Parser::parse(expression).optimize().createProgram();
}
kineticEnergyExpression = Lepton::Parser::parse(integrator.getKineticEnergyExpression()).optimize().createProgram();
kineticEnergyNeedsForce = false;
......@@ -100,27 +97,25 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
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);
// 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");
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++) {
......@@ -132,47 +127,12 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
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;
}
}
}
}
}
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.
......@@ -188,65 +148,54 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
// 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.
for (int step = 0; step < numSteps; ) {
if ((needsForces[step] || needsEnergy[step]) && (!forcesAreValid || context.getLastForceGroups() != forceGroupFlags[step])) {
// Recompute forces and/or energy.
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;
}
bool computeForce = needsForces[step] || computeBothForceAndEnergy[step];
bool computeEnergy = needsEnergy[step] || computeBothForceAndEnergy[step];
recordChangedParameters(context, globals);
RealOpenMM e = context.calcForcesAndEnergy(computeForce, computeEnergy, forceGroup[i]);
RealOpenMM e = context.calcForcesAndEnergy(computeForce, computeEnergy, forceGroupFlags[step]);
if (computeEnergy)
energy = e;
forcesAreValid = true;
}
globals[energyName[i]] = energy;
globals[energyName[step]] = energy;
// Execute the step.
switch (stepType[i]) {
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[i]] = stepExpression[i].evaluate(variables);
globals[stepVariable[step]] = stepExpressions[step][0].evaluate(variables);
break;
}
case CustomIntegrator::ComputePerDof: {
vector<RealVec>* results = NULL;
if (stepVariable[i] == "x")
if (stepVariable[step] == "x")
results = &atomCoordinates;
else if (stepVariable[i] == "v")
else if (stepVariable[step] == "v")
results = &velocities;
else {
for (int j = 0; j < integrator.getNumPerDofVariables(); j++)
if (stepVariable[i] == integrator.getPerDofVariableName(j))
if (stepVariable[step] == 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]);
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, stepExpression[i], forceName[i]);
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[i]] = sum;
globals[stepVariable[step]] = sum;
break;
}
case CustomIntegrator::ConstrainPositions: {
......@@ -262,10 +211,27 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
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[i])
if (invalidatesForces[step])
forcesAreValid = false;
step = nextStep;
}
ReferenceVirtualSites::computePositions(context.getSystem(), atomCoordinates);
incrementTimeStep();
......@@ -277,7 +243,7 @@ void ReferenceCustomDynamics::computePerDof(int numberOfAtoms, vector<RealVec>&
const map<string, RealOpenMM>& globals, const vector<vector<RealVec> >& perDof,
const Lepton::ExpressionProgram& expression, const std::string& forceName) {
// Loop over all degrees of freedom.
map<string, RealOpenMM> variables = globals;
for (int i = 0; i < numberOfAtoms; i++) {
if (masses[i] != 0.0) {
......@@ -298,6 +264,29 @@ void ReferenceCustomDynamics::computePerDof(int numberOfAtoms, vector<RealVec>&
}
}
bool ReferenceCustomDynamics::evaluateCondition(int step, map<string, RealOpenMM>& globals) {
map<string, RealOpenMM> variables = globals;
variables["uniform"] = SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber();
variables["gaussian"] = SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
double lhs = stepExpressions[step][0].evaluate(variables);
double rhs = stepExpressions[step][1].evaluate(variables);
switch (comparisons[step]) {
case CustomIntegratorUtilities::EQUAL:
return (lhs == rhs);
case CustomIntegratorUtilities::LESS_THAN:
return (lhs < rhs);
case CustomIntegratorUtilities::GREATER_THAN:
return (lhs > rhs);
case CustomIntegratorUtilities::NOT_EQUAL:
return (lhs != rhs);
case CustomIntegratorUtilities::LESS_THAN_OR_EQUAL:
return (lhs <= rhs);
case CustomIntegratorUtilities::GREATER_THAN_OR_EQUAL:
return (lhs >= rhs);
}
throw OpenMMException("ReferenceCustomDynamics: Invalid comparison operator");
}
/**
* Check which context parameters have changed and register them with the context.
*/
......
platforms/reference/tests/TestReferenceCustomIntegrator.cpp
View file @ 44b96f0c
......@@ -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) 2008-2013 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -688,6 +688,67 @@ void testRespa() {
}
}
void testIfBlock() {
System system;
system.addParticle(2.0);
system.addParticle(2.0);
const double dt = 0.01;
CustomIntegrator integrator(dt);
integrator.addGlobalVariable("a", 0);
integrator.addGlobalVariable("b", 0);
integrator.addComputeGlobal("b", "1");
integrator.beginIfBlock("a < 3.5");
integrator.addComputeGlobal("b", "a+1");
integrator.endBlock();
Context context(system, integrator, platform);
// Set "a" to 1.7 and verify that "b" gets set to a+1.
integrator.setGlobalVariable(0, 1.7);
integrator.step(1);
ASSERT_EQUAL_TOL(2.7, integrator.getGlobalVariable(1), 1e-6);
// Now set it to a value that should cause the block to be skipped.
integrator.setGlobalVariable(0, 4.1);
integrator.step(1);
ASSERT_EQUAL_TOL(1.0, integrator.getGlobalVariable(1), 1e-6);
}
void testWhileBlock() {
System system;
system.addParticle(2.0);
system.addParticle(2.0);
const double dt = 0.01;
CustomIntegrator integrator(dt);
integrator.addGlobalVariable("a", 0);
integrator.addGlobalVariable("b", 0);
integrator.addComputeGlobal("b", "1");
integrator.beginWhileBlock("b <= a");
integrator.addComputeGlobal("b", "b+1");
integrator.endBlock();
Context context(system, integrator, platform);
// Try a case where the loop should be skipped.
integrator.setGlobalVariable(0, -3.3);
integrator.step(1);
ASSERT_EQUAL_TOL(1.0, integrator.getGlobalVariable(1), 1e-6);
// In this case it should be executed exactly once.
integrator.setGlobalVariable(0, 1.2);
integrator.step(1);
ASSERT_EQUAL_TOL(2.0, integrator.getGlobalVariable(1), 1e-6);
// In this case, it should be executed several times.
integrator.setGlobalVariable(0, 5.3);
integrator.step(1);
ASSERT_EQUAL_TOL(6.0, integrator.getGlobalVariable(1), 1e-6);
}
int main() {
try {
testSingleBond();
......@@ -702,6 +763,8 @@ int main() {
testPerDofVariables();
testForceGroups();
testRespa();
testIfBlock();
testWhileBlock();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
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