Merge pull request #173 from peastman/master

Performance improvements to CPU implementation of custom forces

libraries/lepton/include/Lepton.h

@@ -32,6 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#include "lepton/CompiledExpression.h"
 #include "lepton/CustomFunction.h"
 #include "lepton/ExpressionProgram.h"
 #include "lepton/ExpressionTreeNode.h"

libraries/lepton/include/lepton/CompiledExpression.h

+#ifndef LEPTON_COMPILED_EXPRESSION_H_
+#define LEPTON_COMPILED_EXPRESSION_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   Lepton                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the Lepton expression parser originating from              *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2013 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "ExpressionTreeNode.h"
+#include "windowsIncludes.h"
+#include <map>
+#include <set>
+#include <string>
+#include <vector>
+
+namespace Lepton {
+
+class Operation;
+class ParsedExpression;
+
+/**
+ * A CompiledExpression is a highly optimized representation of an expression for cases when you want to evaluate
+ * it many times as quickly as possible.  You should treat it as an opaque object; none of the internal representation
+ * is visible.
+ * 
+ * A CompiledExpression is created by calling createCompiledExpression() on a ParsedExpression.
+ */
+
+class LEPTON_EXPORT CompiledExpression {
+public:
+    CompiledExpression();
+    CompiledExpression(const CompiledExpression& expression);
+    ~CompiledExpression();
+    CompiledExpression& operator=(const CompiledExpression& expression);
+    /**
+     * Get the names of all variables used by this expression.
+     */
+    const std::set<std::string>& getVariables() const;
+    /**
+     * Get a reference to the memory location where the value of a particular variable is stored.  This can be used
+     * to set the value of the variable before calling evaluate().
+     */
+    double& getVariableReference(const std::string& name);
+    /**
+     * Evaluate the expression.  The values of all variables should have been set before calling this.
+     */
+    double evaluate() const;
+private:
+    friend class ParsedExpression;
+    CompiledExpression(const ParsedExpression& expression);
+    void compileExpression(const ExpressionTreeNode& node, std::vector<std::pair<ExpressionTreeNode, int> >& temps);
+    int findTempIndex(const ExpressionTreeNode& node, std::vector<std::pair<ExpressionTreeNode, int> >& temps);
+    std::vector<std::vector<int> > arguments;
+    std::vector<int> target;
+    std::vector<Operation*> operation;
+    std::map<std::string, int> variableIndices;
+    std::set<std::string> variableNames;
+    mutable std::vector<double> workspace;
+    mutable std::vector<double> argValues;
+    std::map<std::string, double> dummyVariables;
+};
+
+} // namespace Lepton
+
+#endif /*LEPTON_COMPILED_EXPRESSION_H_*/

libraries/lepton/include/lepton/ExpressionProgram.h

@@ -48,9 +48,7 @@ class ParsedExpression;
  * evaluated and the result is pushed back onto the stack.  At the end, the stack contains a single value,
  * which is the value of the expression.
  *
- * An ExpressionProgram is created by calling createProgram() on a ParsedExpression.  It can generally be evaluated
- * more quickly than the ParsedExpression itself, so when you need to evaluate an expression many times, it is
- * most efficient to create an ExpressionProgram from it.
+ * An ExpressionProgram is created by calling createProgram() on a ParsedExpression.
  */
 
 class LEPTON_EXPORT ExpressionProgram {

libraries/lepton/include/lepton/Operation.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2009 Stanford University and the Authors.           *
+ * Portions copyright (c) 2009-2013 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -965,6 +965,8 @@ private:
 class LEPTON_EXPORT Operation::PowerConstant : public Operation {
 public:
     PowerConstant(double value) : value(value) {
+        intValue = (int) value;
+        isIntPower = (intValue == value);
     }
     std::string getName() const {
         std::stringstream name;
@@ -981,7 +983,26 @@ public:
         return new PowerConstant(value);
     }
     double evaluate(double* args, const std::map<std::string, double>& variables) const {
-        return std::pow(args[0], value);
+        if (isIntPower) {
+            // Integer powers can be computed much more quickly by repeated multiplication.
+            
+            int exponent = intValue;
+            double base = args[0];
+            if (exponent < 0) {
+                exponent = -exponent;
+                base = 1.0/base;
+            }
+            double result = 1.0;
+            while (exponent != 0) {
+                if ((exponent&1) == 1)
+                    result *= base;
+                base *= base;
+                exponent = exponent>>1;
+           }
+           return result;
+        }
+        else
+            return std::pow(args[0], value);
     }
     ExpressionTreeNode differentiate(const std::vector<ExpressionTreeNode>& children, const std::vector<ExpressionTreeNode>& childDerivs, const std::string& variable) const;
     double getValue() const {
@@ -996,6 +1017,8 @@ public:
     }
 private:
     double value;
+    int intValue;
+    bool isIntPower;
 };
 
 class LEPTON_EXPORT Operation::Min : public Operation {

libraries/lepton/include/lepton/ParsedExpression.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2009 Stanford University and the Authors.           *
+ * Portions copyright (c) 2009=2013 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -39,6 +39,7 @@
 
 namespace Lepton {
 
+class CompiledExpression;
 class ExpressionProgram;
 
 /**
@@ -97,6 +98,10 @@ public:
      * Create an ExpressionProgram that represents the same calculation as this expression.
      */
     ExpressionProgram createProgram() const;
+    /**
+     * Create a CompiledExpression that represents the same calculation as this expression.
+     */
+    CompiledExpression createCompiledExpression() const;
     /**
      * Create a new ParsedExpression which is identical to this one, except that the names of some
      * variables have been changed.

libraries/lepton/src/CompiledExpression.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   Lepton                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the Lepton expression parser originating from              *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2013 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "lepton/CompiledExpression.h"
+#include "lepton/Operation.h"
+#include "lepton/ParsedExpression.h"
+#include <utility>
+
+using namespace Lepton;
+using namespace std;
+
+CompiledExpression::CompiledExpression() {
+}
+
+CompiledExpression::CompiledExpression(const ParsedExpression& expression) {
+    ParsedExpression expr = expression.optimize(); // Just in case it wasn't already optimized.
+    vector<pair<ExpressionTreeNode, int> > temps;
+    compileExpression(expr.getRootNode(), temps);
+}
+
+CompiledExpression::~CompiledExpression() {
+    for (int i = 0; i < (int) operation.size(); i++)
+        if (operation[i] != NULL)
+            delete operation[i];
+}
+
+CompiledExpression::CompiledExpression(const CompiledExpression& expression) {
+    *this = expression;
+}
+
+CompiledExpression& CompiledExpression::operator=(const CompiledExpression& expression) {
+    arguments = expression.arguments;
+    target = expression.target;
+    variableIndices = expression.variableIndices;
+    variableNames = expression.variableNames;
+    workspace.resize(expression.workspace.size());
+    argValues.resize(expression.argValues.size());
+    operation.resize(expression.operation.size());
+    for (int i = 0; i < (int) operation.size(); i++)
+        operation[i] = expression.operation[i]->clone();
+    return *this;
+}
+
+void CompiledExpression::compileExpression(const ExpressionTreeNode& node, vector<pair<ExpressionTreeNode, int> >& temps) {
+    if (findTempIndex(node, temps) != -1)
+        return; // We have already processed a node identical to this one.
+    
+    // Process the child nodes.
+    
+    vector<int> args;
+    for (int i = 0; i < node.getChildren().size(); i++) {
+        compileExpression(node.getChildren()[i], temps);
+        args.push_back(findTempIndex(node.getChildren()[i], temps));
+    }
+    
+    // Process this node.
+    
+    if (node.getOperation().getId() == Operation::VARIABLE) {
+        variableIndices[node.getOperation().getName()] = workspace.size();
+        variableNames.insert(node.getOperation().getName());
+    }
+    else {
+        int stepIndex = arguments.size();
+        arguments.push_back(vector<int>());
+        target.push_back(workspace.size());
+        operation.push_back(node.getOperation().clone());
+        if (args.size() == 0)
+            arguments[stepIndex].push_back(0); // The value won't actually be used.  We just need something there.
+        else {
+            // If the arguments are sequential, we can just pass a pointer to the first one.
+            
+            bool sequential = true;
+            for (int i = 1; i < args.size(); i++)
+                if (args[i] != args[i-1]+1)
+                    sequential = false;
+            if (sequential)
+                arguments[stepIndex].push_back(args[0]);
+            else {
+                arguments[stepIndex] = args;
+                if (args.size() > argValues.size())
+                    argValues.resize(args.size(), 0.0);
+            }
+        }
+    }
+    temps.push_back(make_pair(node, workspace.size()));
+    workspace.push_back(0.0);
+}
+
+int CompiledExpression::findTempIndex(const ExpressionTreeNode& node, vector<pair<ExpressionTreeNode, int> >& temps) {
+    for (int i = 0; i < (int) temps.size(); i++)
+        if (temps[i].first == node)
+            return i;
+    return -1;
+}
+
+const set<string>& CompiledExpression::getVariables() const {
+    return variableNames;
+}
+
+double& CompiledExpression::getVariableReference(const string& name) {
+    map<string, int>::iterator index = variableIndices.find(name);
+    if (index == variableIndices.end())
+        throw Exception("getVariableReference: Unknown variable '"+name+"'");
+    return workspace[index->second];
+}
+
+double CompiledExpression::evaluate() const {
+    // Loop over the operations and evaluate each one.
+    
+    for (int step = 0; step < operation.size(); step++) {
+        const vector<int>& args = arguments[step];
+        if (args.size() == 1)
+            workspace[target[step]] = operation[step]->evaluate(&workspace[args[0]], dummyVariables);
+        else {
+            for (int i = 0; i < args.size(); i++)
+                argValues[i] = workspace[args[i]];
+            workspace[target[step]] = operation[step]->evaluate(&argValues[0], dummyVariables);
+        }
+    }
+    return workspace[workspace.size()-1];
+}

libraries/lepton/src/ExpressionProgram.cpp

@@ -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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2009-2013 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -93,14 +93,13 @@ double ExpressionProgram::evaluate() const {
 }
 
 double ExpressionProgram::evaluate(const std::map<std::string, double>& variables) const {
-    vector<double> args(max(maxArgs, 1));
-    vector<double> stack(stackSize);
-    int stackPointer = 0;
+    vector<double> stack(stackSize+1);
+    int stackPointer = stackSize;
     for (int i = 0; i < (int) operations.size(); i++) {
         int numArgs = operations[i]->getNumArguments();
-        for (int j = 0; j < numArgs; j++)
-            args[j] = stack[--stackPointer];
-        stack[stackPointer++] = operations[i]->evaluate(&args[0], variables);
+        double result = operations[i]->evaluate(&stack[stackPointer], variables);
+        stackPointer += numArgs-1;
+        stack[stackPointer] = result;
     }
-    return stack[0];
+    return stack[stackSize-1];
 }

libraries/lepton/src/ParsedExpression.cpp

@@ -30,6 +30,7 @@
  * -------------------------------------------------------------------------- */
 
 #include "lepton/ParsedExpression.h"
+#include "lepton/CompiledExpression.h"
 #include "lepton/ExpressionProgram.h"
 #include "lepton/Operation.h"
 #include <limits>
@@ -294,6 +295,10 @@ ExpressionProgram ParsedExpression::createProgram() const {
     return ExpressionProgram(*this);
 }
 
+CompiledExpression ParsedExpression::createCompiledExpression() const {
+    return CompiledExpression(*this);
+}
+
 ParsedExpression ParsedExpression::renameVariables(const map<string, string>& replacements) const {
     return ParsedExpression(renameNodeVariables(getRootNode(), replacements));
 }

openmmapi/include/openmm/internal/CustomNonbondedForceImpl.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2013 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -35,7 +35,7 @@
 #include "ForceImpl.h"
 #include "openmm/CustomNonbondedForce.h"
 #include "openmm/Kernel.h"
-#include "lepton/ExpressionProgram.h"
+#include "lepton/CompiledExpression.h"
 #include <utility>
 #include <map>
 #include <string>
@@ -68,7 +68,7 @@ public:
     static double calcLongRangeCorrection(const CustomNonbondedForce& force, const Context& context);
 private:
     class TabulatedFunction;
-    static double integrateInteraction(const Lepton::ExpressionProgram& expression, const std::vector<double>& params1, const std::vector<double>& params2,
+    static double integrateInteraction(Lepton::CompiledExpression& expression, const std::vector<double>& params1, const std::vector<double>& params2,
             const CustomNonbondedForce& force, const Context& context);
     const CustomNonbondedForce& owner;
     Kernel kernel;

openmmapi/src/CustomNonbondedForceImpl.cpp

@@ -182,7 +182,7 @@ double CustomNonbondedForceImpl::calcLongRangeCorrection(const CustomNonbondedFo
         force.getFunctionParameters(i, name, values, min, max);
         functions[name] = new TabulatedFunction(min, max, values);
     }
-    Lepton::ExpressionProgram expression = Lepton::Parser::parse(force.getEnergyFunction(), functions).optimize().createProgram();
+    Lepton::CompiledExpression expression = Lepton::Parser::parse(force.getEnergyFunction(), functions).createCompiledExpression();
     
     // Identify all particle classes (defined by parameters), and record the class of each particle.
     
@@ -251,25 +251,35 @@ double CustomNonbondedForceImpl::calcLongRangeCorrection(const CustomNonbondedFo
     return 2*M_PI*numParticles*numParticles*sum;
 }
 
-double CustomNonbondedForceImpl::integrateInteraction(const Lepton::ExpressionProgram& expression, const vector<double>& params1, const vector<double>& params2,
+double CustomNonbondedForceImpl::integrateInteraction(Lepton::CompiledExpression& expression, const vector<double>& params1, const vector<double>& params2,
         const CustomNonbondedForce& force, const Context& context) {
-    map<std::string, double> variables;
+    const set<string>& variables = expression.getVariables();
     for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
         stringstream name1, name2;
         name1 << force.getPerParticleParameterName(i) << 1;
         name2 << force.getPerParticleParameterName(i) << 2;
-        variables[name1.str()] = params1[i];
-        variables[name2.str()] = params2[i];
+        if (variables.find(name1.str()) != variables.end())
+            expression.getVariableReference(name1.str()) = params1[i];
+        if (variables.find(name2.str()) != variables.end())
+            expression.getVariableReference(name2.str()) = params2[i];
     }
     for (int i = 0; i < force.getNumGlobalParameters(); i++) {
         const string& name = force.getGlobalParameterName(i);
-        variables[name] = context.getParameter(name);
+        if (variables.find(name) != variables.end())
+            expression.getVariableReference(name) = context.getParameter(name);
     }
     
     // To integrate from r_cutoff to infinity, make the change of variables x=r_cutoff/r and integrate from 0 to 1.
     // This introduces another r^2 into the integral, which along with the r^2 in the formula for the correction
     // means we multiply the function by r^4.  Use the midpoint method.
 
+    double* rPointer;
+    try {
+        rPointer = &expression.getVariableReference("r");
+    }
+    catch (exception& ex) {
+        throw OpenMMException("CustomNonbondedForce: Cannot use long range correction with a force that does not depend on r.");
+    }
     double cutoff = force.getCutoffDistance();
     double sum = 0;
     int numPoints = 1;
@@ -281,9 +291,9 @@ double CustomNonbondedForceImpl::integrateInteraction(const Lepton::ExpressionPr
                 continue;
             double x = (i+0.5)/numPoints;
             double r = cutoff/x;
-            variables["r"] = r;
+            *rPointer = r;
             double r2 = r*r;
-            newSum += expression.evaluate(variables)*r2*r2;
+            newSum += expression.evaluate()*r2*r2;
         }
         sum = newSum/numPoints + oldSum/3;
         if (iteration > 2 && (fabs((sum-oldSum)/sum) < 1e-5 || sum == 0))
@@ -309,8 +319,8 @@ double CustomNonbondedForceImpl::integrateInteraction(const Lepton::ExpressionPr
                 double x = (i+0.5)/numPoints;
                 double r = rswitch+x*(cutoff-rswitch);
                 double switchValue = x*x*x*(10+x*(-15+x*6));
-                variables["r"] = r;
-                newSum += switchValue*expression.evaluate(variables)*r*r;
+                *rPointer = r;
+                newSum += switchValue*expression.evaluate()*r*r;
             }
             sum2 = newSum/numPoints + oldSum/3;
             if (iteration > 2 && (fabs((sum2-oldSum)/sum2) < 1e-5 || sum2 == 0))

platforms/reference/include/ReferenceCustomAngleIxn.h

-/* Portions copyright (c) 2010 Stanford University and Simbios.
+/* Portions copyright (c) 2010-2013 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -25,17 +25,20 @@
 #define __ReferenceCustomAngleIxn_H__
 
 #include "ReferenceBondIxn.h"
-#include "lepton/ExpressionProgram.h"
+#include "lepton/CompiledExpression.h"
 
 // ---------------------------------------------------------------------------------------
 
 class ReferenceCustomAngleIxn : public ReferenceBondIxn {
 
    private:
-      Lepton::ExpressionProgram energyExpression;
-      Lepton::ExpressionProgram forceExpression;
-      std::vector<std::string> paramNames;
-      std::map<std::string, double> globalParameters;
+      Lepton::CompiledExpression energyExpression;
+      Lepton::CompiledExpression forceExpression;
+      std::vector<double*> energyParams;
+      std::vector<double*> forceParams;
+      double* energyTheta;
+      double* forceTheta;
+      int numParameters;
 
    public:
 
@@ -45,7 +48,7 @@ class ReferenceCustomAngleIxn : public ReferenceBondIxn {
 
          --------------------------------------------------------------------------------------- */
 
-       ReferenceCustomAngleIxn(const Lepton::ExpressionProgram& energyExpression, const Lepton::ExpressionProgram& forceExpression,
+       ReferenceCustomAngleIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
                               const std::vector<std::string>& parameterNames, std::map<std::string, double> globalParameters);
 
       /**---------------------------------------------------------------------------------------

platforms/reference/include/ReferenceCustomBondIxn.h

 
-/* Portions copyright (c) 2009 Stanford University and Simbios.
+/* Portions copyright (c) 2009-2013 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -26,17 +26,20 @@
 #define __ReferenceCustomBondIxn_H__
 
 #include "ReferenceBondIxn.h"
-#include "lepton/ExpressionProgram.h"
+#include "lepton/CompiledExpression.h"
 
 // ---------------------------------------------------------------------------------------
 
 class ReferenceCustomBondIxn : public ReferenceBondIxn {
 
    private:
-      Lepton::ExpressionProgram energyExpression;
-      Lepton::ExpressionProgram forceExpression;
-      std::vector<std::string> paramNames;
-      std::map<std::string, double> globalParameters;
+      Lepton::CompiledExpression energyExpression;
+      Lepton::CompiledExpression forceExpression;
+      std::vector<double*> energyParams;
+      std::vector<double*> forceParams;
+      double* energyR;
+      double* forceR;
+      int numParameters;
 
    public:
 
@@ -46,7 +49,7 @@ class ReferenceCustomBondIxn : public ReferenceBondIxn {
 
          --------------------------------------------------------------------------------------- */
 
-       ReferenceCustomBondIxn(const Lepton::ExpressionProgram& energyExpression, const Lepton::ExpressionProgram& forceExpression,
+       ReferenceCustomBondIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
                               const std::vector<std::string>& parameterNames, std::map<std::string, double> globalParameters);
 
       /**---------------------------------------------------------------------------------------

platforms/reference/include/ReferenceCustomExternalIxn.h

 
-/* Portions copyright (c) 2009 Stanford University and Simbios.
+/* Portions copyright (c) 2009-2013 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -26,19 +26,26 @@
 #define __ReferenceCustomExternalIxn_H__
 
 #include "ReferenceCustomExternalIxn.h"
-#include "lepton/ExpressionProgram.h"
+#include "lepton/CompiledExpression.h"
 
 // ---------------------------------------------------------------------------------------
 
 class ReferenceCustomExternalIxn {
 
    private:
-      Lepton::ExpressionProgram energyExpression;
-      Lepton::ExpressionProgram forceExpressionX;
-      Lepton::ExpressionProgram forceExpressionY;
-      Lepton::ExpressionProgram forceExpressionZ;
-      std::vector<std::string> paramNames;
-      std::map<std::string, double> globalParameters;
+      Lepton::CompiledExpression energyExpression;
+      Lepton::CompiledExpression forceExpressionX;
+      Lepton::CompiledExpression forceExpressionY;
+      Lepton::CompiledExpression forceExpressionZ;
+      std::vector<double*> energyParams;
+      std::vector<double*> forceXParams;
+      std::vector<double*> forceYParams;
+      std::vector<double*> forceZParams;
+      double *energyX, *energyY, *energyZ;
+      double *forceXX, *forceXY, *forceXZ;
+      double *forceYX, *forceYY, *forceYZ;
+      double *forceZX, *forceZY, *forceZZ;
+      int numParameters;
 
    public:
 
@@ -48,8 +55,8 @@ class ReferenceCustomExternalIxn {
 
          --------------------------------------------------------------------------------------- */
 
-       ReferenceCustomExternalIxn(const Lepton::ExpressionProgram& energyExpression, const Lepton::ExpressionProgram& forceExpressionX,
-                              const Lepton::ExpressionProgram& forceExpressionY, const Lepton::ExpressionProgram& forceExpressionZ,
+       ReferenceCustomExternalIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpressionX,
+                              const Lepton::CompiledExpression& forceExpressionY, const Lepton::CompiledExpression& forceExpressionZ,
                               const std::vector<std::string>& parameterNames, std::map<std::string, double> globalParameters);
 
       /**---------------------------------------------------------------------------------------

platforms/reference/include/ReferenceCustomNonbondedIxn.h

 
-/* Portions copyright (c) 2009 Stanford University and Simbios.
+/* Portions copyright (c) 2009-2013 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -27,7 +27,7 @@
 
 #include "ReferencePairIxn.h"
 #include "ReferenceNeighborList.h"
-#include "lepton/ExpressionProgram.h"
+#include "lepton/CompiledExpression.h"
 #include <map>
 #include <set>
 #include <utility>
@@ -45,10 +45,13 @@ class ReferenceCustomNonbondedIxn {
       const OpenMM::NeighborList* neighborList;
       RealOpenMM periodicBoxSize[3];
       RealOpenMM cutoffDistance, switchingDistance;
-      Lepton::ExpressionProgram energyExpression;
-      Lepton::ExpressionProgram forceExpression;
+      Lepton::CompiledExpression energyExpression;
+      Lepton::CompiledExpression forceExpression;
       std::vector<std::string> paramNames;
-      std::vector<std::string> particleParamNames;
+      std::vector<double*> energyParticleParams;
+      std::vector<double*> forceParticleParams;
+      double* energyR;
+      double* forceR;
       std::vector<std::pair<std::set<int>, std::set<int> > > interactionGroups;
 
       /**---------------------------------------------------------------------------------------
@@ -65,9 +68,8 @@ class ReferenceCustomNonbondedIxn {
 
          --------------------------------------------------------------------------------------- */
 
-      void calculateOneIxn( int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates,
-                            std::map<std::string, double>& variables, std::vector<OpenMM::RealVec>& forces,
-                            RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const;
+      void calculateOneIxn( int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& forces,
+                            RealOpenMM* energyByAtom, RealOpenMM* totalEnergy );
 
 
    public:
@@ -78,7 +80,7 @@ class ReferenceCustomNonbondedIxn {
 
          --------------------------------------------------------------------------------------- */
 
-       ReferenceCustomNonbondedIxn(const Lepton::ExpressionProgram& energyExpression, const Lepton::ExpressionProgram& forceExpression,
+       ReferenceCustomNonbondedIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
                                    const std::vector<std::string>& parameterNames);
 
       /**---------------------------------------------------------------------------------------
@@ -153,7 +155,7 @@ class ReferenceCustomNonbondedIxn {
       void calculatePairIxn( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
                             RealOpenMM** atomParameters, std::vector<std::set<int> >& exclusions,
                             RealOpenMM* fixedParameters, const std::map<std::string, double>& globalParameters,
-                            std::vector<OpenMM::RealVec>& forces, RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const;
+                            std::vector<OpenMM::RealVec>& forces, RealOpenMM* energyByAtom, RealOpenMM* totalEnergy );
 
 // ---------------------------------------------------------------------------------------
 

platforms/reference/include/ReferenceCustomTorsionIxn.h

-/* Portions copyright (c) 2010 Stanford University and Simbios.
+/* Portions copyright (c) 2010-2013 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -25,17 +25,20 @@
 #define __ReferenceCustomTorsionIxn_H__
 
 #include "ReferenceBondIxn.h"
-#include "lepton/ExpressionProgram.h"
+#include "lepton/CompiledExpression.h"
 
 // ---------------------------------------------------------------------------------------
 
 class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
 
    private:
-      Lepton::ExpressionProgram energyExpression;
-      Lepton::ExpressionProgram forceExpression;
-      std::vector<std::string> paramNames;
-      std::map<std::string, double> globalParameters;
+      Lepton::CompiledExpression energyExpression;
+      Lepton::CompiledExpression forceExpression;
+      std::vector<double*> energyParams;
+      std::vector<double*> forceParams;
+      double* energyTheta;
+      double* forceTheta;
+      int numParameters;
 
    public:
 
@@ -45,7 +48,7 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
 
          --------------------------------------------------------------------------------------- */
 
-       ReferenceCustomTorsionIxn(const Lepton::ExpressionProgram& energyExpression, const Lepton::ExpressionProgram& forceExpression,
+       ReferenceCustomTorsionIxn(const Lepton::CompiledExpression& energyExpression, const Lepton::CompiledExpression& forceExpression,
                               const std::vector<std::string>& parameterNames, std::map<std::string, double> globalParameters);
 
       /**---------------------------------------------------------------------------------------

platforms/reference/include/ReferenceForce.h

-
-/* Portions copyright (c) 2006 Stanford University and Simbios.
+/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
  * Contributors: Pande Group
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -25,6 +24,7 @@
 #ifndef __ReferenceForce_H__
 #define __ReferenceForce_H__
 
+#include "lepton/CompiledExpression.h"
 #include "openmm/internal/windowsExport.h"
 
 // ---------------------------------------------------------------------------------------
@@ -109,6 +109,18 @@ class OPENMM_EXPORT  ReferenceForce {
       
       static void getDeltaROnly( const RealOpenMM* atomCoordinatesI, const RealOpenMM* atomCoordinatesJ,
                                 RealOpenMM* deltaR );
+
+      /**
+       * Get a pointer to the memory for setting a variable in a CompiledExpression.  If the expression
+       * does not use the specified variable, return NULL.
+       */
+      static double* getVariablePointer(Lepton::CompiledExpression& expression, const std::string& name);
+
+      /**
+       * Set the value of a variable in a CompiledExpression, using the pointer that was returned by getVariablePointer().
+       */
+      static void setVariable(double* pointer, double value);
+
 };
 
 // ---------------------------------------------------------------------------------------

platforms/reference/include/ReferenceKernels.h

@@ -36,6 +36,7 @@
 #include "openmm/kernels.h"
 #include "SimTKOpenMMRealType.h"
 #include "ReferenceNeighborList.h"
+#include "lepton/CompiledExpression.h"
 #include "lepton/ExpressionProgram.h"
 
 class CpuObc;
@@ -316,7 +317,7 @@ private:
     int numBonds;
     int **bondIndexArray;
     RealOpenMM **bondParamArray;
-    Lepton::ExpressionProgram energyExpression, forceExpression;
+    Lepton::CompiledExpression energyExpression, forceExpression;
     std::vector<std::string> parameterNames, globalParameterNames;
 };
 
@@ -392,7 +393,7 @@ private:
     int numAngles;
     int **angleIndexArray;
     RealOpenMM **angleParamArray;
-    Lepton::ExpressionProgram energyExpression, forceExpression;
+    Lepton::CompiledExpression energyExpression, forceExpression;
     std::vector<std::string> parameterNames, globalParameterNames;
 };
 
@@ -534,7 +535,7 @@ private:
     int numTorsions;
     int **torsionIndexArray;
     RealOpenMM **torsionParamArray;
-    Lepton::ExpressionProgram energyExpression, forceExpression;
+    Lepton::CompiledExpression energyExpression, forceExpression;
     std::vector<std::string> parameterNames, globalParameterNames;
 };
 
@@ -621,7 +622,7 @@ private:
     CustomNonbondedForce* forceCopy;
     std::map<std::string, double> globalParamValues;
     std::vector<std::set<int> > exclusions;
-    Lepton::ExpressionProgram energyExpression, forceExpression;
+    Lepton::CompiledExpression energyExpression, forceExpression;
     std::vector<std::string> parameterNames, globalParameterNames;
     std::vector<std::pair<std::set<int>, std::set<int> > > interactionGroups;
     NonbondedMethod nonbondedMethod;
@@ -781,7 +782,7 @@ private:
     int numParticles;
     std::vector<int> particles;
     RealOpenMM **particleParamArray;
-    Lepton::ExpressionProgram energyExpression, forceExpressionX, forceExpressionY, forceExpressionZ;
+    Lepton::CompiledExpression energyExpression, forceExpressionX, forceExpressionY, forceExpressionZ;
     std::vector<std::string> parameterNames, globalParameterNames;
 };
 

platforms/reference/src/ReferenceKernels.cpp

@@ -420,8 +420,8 @@ void ReferenceCalcCustomBondForceKernel::initialize(const System& system, const
     // Parse the expression used to calculate the force.
 
     Lepton::ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
-    energyExpression = expression.createProgram();
-    forceExpression = expression.differentiate("r").optimize().createProgram();
+    energyExpression = expression.createCompiledExpression();
+    forceExpression = expression.differentiate("r").createCompiledExpression();
     for (int i = 0; i < numParameters; i++)
         parameterNames.push_back(force.getPerBondParameterName(i));
     for (int i = 0; i < force.getNumGlobalParameters(); i++)
@@ -534,8 +534,8 @@ void ReferenceCalcCustomAngleForceKernel::initialize(const System& system, const
     // Parse the expression used to calculate the force.
 
     Lepton::ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
-    energyExpression = expression.createProgram();
-    forceExpression = expression.differentiate("theta").optimize().createProgram();
+    energyExpression = expression.createCompiledExpression();
+    forceExpression = expression.differentiate("theta").createCompiledExpression();
     for (int i = 0; i < numParameters; i++)
         parameterNames.push_back(force.getPerAngleParameterName(i));
     for (int i = 0; i < force.getNumGlobalParameters(); i++)
@@ -744,8 +744,8 @@ void ReferenceCalcCustomTorsionForceKernel::initialize(const System& system, con
     // Parse the expression used to calculate the force.
 
     Lepton::ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
-    energyExpression = expression.createProgram();
-    forceExpression = expression.differentiate("theta").optimize().createProgram();
+    energyExpression = expression.createCompiledExpression();
+    forceExpression = expression.differentiate("theta").createCompiledExpression();
     for (int i = 0; i < numParameters; i++)
         parameterNames.push_back(force.getPerTorsionParameterName(i));
     for (int i = 0; i < force.getNumGlobalParameters(); i++)
@@ -1028,8 +1028,8 @@ void ReferenceCalcCustomNonbondedForceKernel::initialize(const System& system, c
     // Parse the various expressions used to calculate the force.
 
     Lepton::ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction(), functions).optimize();
-    energyExpression = expression.createProgram();
-    forceExpression = expression.differentiate("r").optimize().createProgram();
+    energyExpression = expression.createCompiledExpression();
+    forceExpression = expression.differentiate("r").createCompiledExpression();
     for (int i = 0; i < numParameters; i++)
         parameterNames.push_back(force.getPerParticleParameterName(i));
     for (int i = 0; i < force.getNumGlobalParameters(); i++) {
@@ -1426,10 +1426,10 @@ void ReferenceCalcCustomExternalForceKernel::initialize(const System& system, co
     // Parse the expression used to calculate the force.
 
     Lepton::ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
-    energyExpression = expression.createProgram();
-    forceExpressionX = expression.differentiate("x").optimize().createProgram();
-    forceExpressionY = expression.differentiate("y").optimize().createProgram();
-    forceExpressionZ = expression.differentiate("z").optimize().createProgram();
+    energyExpression = expression.createCompiledExpression();
+    forceExpressionX = expression.differentiate("x").createCompiledExpression();
+    forceExpressionY = expression.differentiate("y").createCompiledExpression();
+    forceExpressionZ = expression.differentiate("z").createCompiledExpression();
     for (int i = 0; i < numParameters; i++)
         parameterNames.push_back(force.getPerParticleParameterName(i));
     for (int i = 0; i < force.getNumGlobalParameters(); i++)

platforms/reference/src/SimTKReference/ReferenceCustomAngleIxn.cpp

-/* Portions copyright (c) 2010 Stanford University and Simbios.
+/* Portions copyright (c) 2010-2013 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -39,16 +39,21 @@ using namespace std;
 
    --------------------------------------------------------------------------------------- */
 
-ReferenceCustomAngleIxn::ReferenceCustomAngleIxn(const Lepton::ExpressionProgram& energyExpression,
-        const Lepton::ExpressionProgram& forceExpression, const vector<string>& parameterNames, map<string, double> globalParameters) :
-        energyExpression(energyExpression), forceExpression(forceExpression), paramNames(parameterNames), globalParameters(globalParameters) {
-
-   // ---------------------------------------------------------------------------------------
-
-   // static const char* methodName = "\nReferenceCustomAngleIxn::ReferenceCustomAngleIxn";
-
-   // ---------------------------------------------------------------------------------------
-
+ReferenceCustomAngleIxn::ReferenceCustomAngleIxn(const Lepton::CompiledExpression& energyExpression,
+        const Lepton::CompiledExpression& forceExpression, const vector<string>& parameterNames, map<string, double> globalParameters) :
+        energyExpression(energyExpression), forceExpression(forceExpression) {
+    
+    energyTheta = ReferenceForce::getVariablePointer(this->energyExpression, "theta");
+    forceTheta = ReferenceForce::getVariablePointer(this->forceExpression, "theta");
+    numParameters = parameterNames.size();
+    for (int i = 0; i < (int) numParameters; i++) {
+        energyParams.push_back(ReferenceForce::getVariablePointer(this->energyExpression, parameterNames[i]));
+        forceParams.push_back(ReferenceForce::getVariablePointer(this->forceExpression, parameterNames[i]));
+    }
+    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->forceExpression, iter->first), iter->second);
+    }
 }
 
 /**---------------------------------------------------------------------------------------
@@ -91,9 +96,10 @@ void ReferenceCustomAngleIxn::calculateBondIxn( int* atomIndices,
    static const RealOpenMM one         = 1.0;
 
    RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex];
-   map<string, double> variables = globalParameters;
-   for (int i = 0; i < (int) paramNames.size(); ++i)
-       variables[paramNames[i]] = parameters[i];
+   for (int i = 0; i < numParameters; i++) {
+       ReferenceForce::setVariable(energyParams[i], parameters[i]);
+       ReferenceForce::setVariable(forceParams[i], parameters[i]);
+   }
 
    // ---------------------------------------------------------------------------------------
 
@@ -118,12 +124,13 @@ void ReferenceCustomAngleIxn::calculateBondIxn( int* atomIndices,
       angle = PI_M;
    else
       angle = ACOS(cosine);
-   variables["theta"] = angle;
+   ReferenceForce::setVariable(energyTheta, angle);
+   ReferenceForce::setVariable(forceTheta, angle);
 
    // Compute the force and energy, and apply them to the atoms.
    
-   RealOpenMM energy = (RealOpenMM) energyExpression.evaluate(variables);
-   RealOpenMM dEdR = (RealOpenMM) forceExpression.evaluate(variables);
+   RealOpenMM energy = (RealOpenMM) energyExpression.evaluate();
+   RealOpenMM dEdR = (RealOpenMM) forceExpression.evaluate();
    RealOpenMM termA =  dEdR/(deltaR[0][ReferenceForce::R2Index]*rp);
    RealOpenMM termC = -dEdR/(deltaR[1][ReferenceForce::R2Index]*rp);
 

platforms/reference/src/SimTKReference/ReferenceCustomBondIxn.cpp

 
-/* Portions copyright (c) 2009 Stanford University and Simbios.
+/* Portions copyright (c) 2009-2013 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -40,16 +40,20 @@ using namespace OpenMM;
 
    --------------------------------------------------------------------------------------- */
 
-ReferenceCustomBondIxn::ReferenceCustomBondIxn(const Lepton::ExpressionProgram& energyExpression,
-        const Lepton::ExpressionProgram& forceExpression, const vector<string>& parameterNames, map<string, double> globalParameters) :
-        energyExpression(energyExpression), forceExpression(forceExpression), paramNames(parameterNames), globalParameters(globalParameters) {
-
-   // ---------------------------------------------------------------------------------------
-
-   // static const char* methodName = "\nReferenceCustomBondIxn::ReferenceCustomBondIxn";
-
-   // ---------------------------------------------------------------------------------------
-
+ReferenceCustomBondIxn::ReferenceCustomBondIxn(const Lepton::CompiledExpression& energyExpression,
+        const Lepton::CompiledExpression& forceExpression, const vector<string>& parameterNames, map<string, double> globalParameters) :
+        energyExpression(energyExpression), forceExpression(forceExpression) {
+    energyR = ReferenceForce::getVariablePointer(this->energyExpression, "r");
+    forceR = ReferenceForce::getVariablePointer(this->forceExpression, "r");
+    numParameters = parameterNames.size();
+    for (int i = 0; i < (int) numParameters; i++) {
+        energyParams.push_back(ReferenceForce::getVariablePointer(this->energyExpression, parameterNames[i]));
+        forceParams.push_back(ReferenceForce::getVariablePointer(this->forceExpression, parameterNames[i]));
+    }
+    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->forceExpression, iter->first), iter->second);
+    }
 }
 
 /**---------------------------------------------------------------------------------------
@@ -95,9 +99,10 @@ void ReferenceCustomBondIxn::calculateBondIxn( int* atomIndices,
    static const RealOpenMM half        = 0.5;
 
    RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
-   map<string, double> variables = globalParameters;
-   for (int i = 0; i < (int) paramNames.size(); ++i)
-       variables[paramNames[i]] = parameters[i];
+   for (int i = 0; i < numParameters; i++) {
+       ReferenceForce::setVariable(energyParams[i], parameters[i]);
+       ReferenceForce::setVariable(forceParams[i], parameters[i]);
+   }
 
    // ---------------------------------------------------------------------------------------
 
@@ -106,8 +111,10 @@ void ReferenceCustomBondIxn::calculateBondIxn( int* atomIndices,
    int atomAIndex = atomIndices[0];
    int atomBIndex = atomIndices[1];
    ReferenceForce::getDeltaR( atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR );
-   variables["r"]             = deltaR[ReferenceForce::RIndex];
-   RealOpenMM dEdR            = (RealOpenMM) forceExpression.evaluate(variables);
+   
+   ReferenceForce::setVariable(energyR, deltaR[ReferenceForce::RIndex]);
+   ReferenceForce::setVariable(forceR, deltaR[ReferenceForce::RIndex]);
+   RealOpenMM dEdR            = (RealOpenMM) forceExpression.evaluate();
    dEdR                       = deltaR[ReferenceForce::RIndex] > zero ? (dEdR/deltaR[ReferenceForce::RIndex]) : zero;
 
    forces[atomAIndex][0]     += dEdR*deltaR[ReferenceForce::XIndex];
@@ -119,5 +126,5 @@ void ReferenceCustomBondIxn::calculateBondIxn( int* atomIndices,
    forces[atomBIndex][2]     -= dEdR*deltaR[ReferenceForce::ZIndex];
 
    if (totalEnergy != NULL)
-       *totalEnergy += (RealOpenMM) energyExpression.evaluate(variables);
+       *totalEnergy += (RealOpenMM) energyExpression.evaluate();
 }