Merge pull request #337 from peastman/functions

Created new API for tabulated functions

platforms/cuda/tests/TestCudaCustomHbondForce.cpp

@@ -214,7 +214,7 @@ void testCustomFunctions() {
     vector<double> function(2);
     function[0] = 0;
     function[1] = 1;
-    custom->addFunction("foo", function, 0, 10);
+    custom->addTabulatedFunction("foo", new Continuous1DFunction(function, 0, 10));
     system.addForce(custom);
     Context context(system, integrator, platform);
     vector<Vec3> positions(3);

platforms/cuda/tests/TestCudaCustomNonbondedForce.cpp

@@ -7,7 +7,7 @@
  * 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) 2008-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -261,7 +261,7 @@ void testPeriodic() {
     ASSERT_EQUAL_TOL(1.9+1+0.9, state.getPotentialEnergy(), TOL);
 }
 
-void testTabulatedFunction() {
+void testContinuous1DFunction() {
     System system;
     system.addParticle(1.0);
     system.addParticle(1.0);
@@ -271,21 +271,20 @@ void testTabulatedFunction() {
     forceField->addParticle(vector<double>());
     vector<double> table;
     for (int i = 0; i < 21; i++)
-        table.push_back(std::sin(0.25*i));
-    forceField->addFunction("fn", table, 1.0, 6.0);
+        table.push_back(sin(0.25*i));
+    forceField->addTabulatedFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
     system.addForce(forceField);
     Context context(system, integrator, platform);
     vector<Vec3> positions(2);
     positions[0] = Vec3(0, 0, 0);
-    double tol = 0.01;
     for (int i = 1; i < 30; i++) {
         double x = (7.0/30.0)*i;
         positions[1] = Vec3(x, 0, 0);
         context.setPositions(positions);
         State state = context.getState(State::Forces | State::Energy);
         const vector<Vec3>& forces = state.getForces();
-        double force = (x < 1.0 || x > 6.0 ? 0.0 : -std::cos(x-1.0));
-        double energy = (x < 1.0 || x > 6.0 ? 0.0 : std::sin(x-1.0))+1.0;
+        double force = (x < 1.0 || x > 6.0 ? 0.0 : -cos(x-1.0));
+        double energy = (x < 1.0 || x > 6.0 ? 0.0 : sin(x-1.0))+1.0;
         ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], 0.1);
         ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], 0.1);
         ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.02);
@@ -295,11 +294,212 @@ void testTabulatedFunction() {
         positions[1] = Vec3(x, 0, 0);
         context.setPositions(positions);
         State state = context.getState(State::Energy);
-        double energy = (x < 1.0 || x > 6.0 ? 0.0 : std::sin(x-1.0))+1.0;
+        double energy = (x < 1.0 || x > 6.0 ? 0.0 : sin(x-1.0))+1.0;
         ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 1e-4);
     }
 }
 
+void testContinuous2DFunction() {
+    const int xsize = 20;
+    const int ysize = 21;
+    const double xmin = 0.4;
+    const double xmax = 1.5;
+    const double ymin = 0.0;
+    const double ymax = 2.1;
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r,a)+1");
+    forceField->addGlobalParameter("a", 0.0);
+    forceField->addParticle(vector<double>());
+    forceField->addParticle(vector<double>());
+    vector<double> table(xsize*ysize);
+    for (int i = 0; i < xsize; i++) {
+        for (int j = 0; j < ysize; j++) {
+            double x = xmin + i*(xmax-xmin)/xsize;
+            double y = ymin + j*(ymax-ymin)/ysize;
+            table[i+xsize*j] = sin(0.25*x)*cos(0.33*y);
+        }
+    }
+    forceField->addTabulatedFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(0, 0, 0);
+    for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
+        for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
+            positions[1] = Vec3(x, 0, 0);
+            context.setParameter("a", y);
+            context.setPositions(positions);
+            State state = context.getState(State::Forces | State::Energy);
+            const vector<Vec3>& forces = state.getForces();
+            double energy = 1;
+            double force = 0;
+            if (x >= xmin && x <= xmax && y >= ymin && y <= ymax) {
+                energy = sin(0.25*x)*cos(0.33*y)+1.0;
+                force = -0.25*cos(0.25*x)*cos(0.33*y);
+            }
+            ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], 0.1);
+            ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], 0.1);
+            ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.02);
+        }
+    }
+}
+
+void testContinuous3DFunction() {
+    const int xsize = 10;
+    const int ysize = 11;
+    const int zsize = 12;
+    const double xmin = 0.4;
+    const double xmax = 1.1;
+    const double ymin = 0.0;
+    const double ymax = 0.9;
+    const double zmin = 0.2;
+    const double zmax = 1.3;
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r,a,b)+1");
+    forceField->addGlobalParameter("a", 0.0);
+    forceField->addGlobalParameter("b", 0.0);
+    forceField->addParticle(vector<double>());
+    forceField->addParticle(vector<double>());
+    vector<double> table(xsize*ysize*zsize);
+    for (int i = 0; i < xsize; i++) {
+        for (int j = 0; j < ysize; j++) {
+            for (int k = 0; k < zsize; k++) {
+                double x = xmin + i*(xmax-xmin)/xsize;
+                double y = ymin + j*(ymax-ymin)/ysize;
+                double z = zmin + k*(zmax-zmin)/zsize;
+                table[i+xsize*j+xsize*ysize*k] = sin(0.25*x)*cos(0.33*y)*(1+z);
+            }
+        }
+    }
+    forceField->addTabulatedFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(0, 0, 0);
+    for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
+        for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
+            for (double z = zmin-0.15; z < zmax+0.2; z += 0.1) {
+                positions[1] = Vec3(x, 0, 0);
+                context.setParameter("a", y);
+                context.setParameter("b", z);
+                context.setPositions(positions);
+                State state = context.getState(State::Forces | State::Energy);
+                const vector<Vec3>& forces = state.getForces();
+                double energy = 1;
+                double force = 0;
+                if (x >= xmin && x <= xmax && y >= ymin && y <= ymax && z >= zmin && z <= zmax) {
+                    energy = sin(0.25*x)*cos(0.33*y)*(1.0+z)+1.0;
+                    force = -0.25*cos(0.25*x)*cos(0.33*y)*(1.0+z);
+                }
+                ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], 0.1);
+                ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], 0.1);
+                ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.05);
+            }
+        }
+    }
+}
+
+void testDiscrete1DFunction() {
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r-1)+1");
+    forceField->addParticle(vector<double>());
+    forceField->addParticle(vector<double>());
+    vector<double> table;
+    for (int i = 0; i < 21; i++)
+        table.push_back(sin(0.25*i));
+    forceField->addTabulatedFunction("fn", new Discrete1DFunction(table));
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(0, 0, 0);
+    for (int i = 0; i < (int) table.size(); i++) {
+        positions[1] = Vec3(i+1, 0, 0);
+        context.setPositions(positions);
+        State state = context.getState(State::Forces | State::Energy);
+        const vector<Vec3>& forces = state.getForces();
+        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[0], 1e-6);
+        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], 1e-6);
+        ASSERT_EQUAL_TOL(table[i]+1.0, state.getPotentialEnergy(), 1e-6);
+    }
+}
+
+void testDiscrete2DFunction() {
+    const int xsize = 10;
+    const int ysize = 5;
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r-1,a)+1");
+    forceField->addGlobalParameter("a", 0.0);
+    forceField->addParticle(vector<double>());
+    forceField->addParticle(vector<double>());
+    vector<double> table;
+    for (int i = 0; i < xsize; i++)
+        for (int j = 0; j < ysize; j++)
+            table.push_back(sin(0.25*i)+cos(0.33*j));
+    forceField->addTabulatedFunction("fn", new Discrete2DFunction(xsize, ysize, table));
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(0, 0, 0);
+    for (int i = 0; i < (int) table.size(); i++) {
+        positions[1] = Vec3((i%xsize)+1, 0, 0);
+        context.setPositions(positions);
+        context.setParameter("a", i/xsize);
+        State state = context.getState(State::Forces | State::Energy);
+        const vector<Vec3>& forces = state.getForces();
+        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[0], 1e-6);
+        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], 1e-6);
+        ASSERT_EQUAL_TOL(table[i]+1.0, state.getPotentialEnergy(), 1e-6);
+    }
+}
+
+void testDiscrete3DFunction() {
+    const int xsize = 8;
+    const int ysize = 5;
+    const int zsize = 6;
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r-1,a,b)+1");
+    forceField->addGlobalParameter("a", 0.0);
+    forceField->addGlobalParameter("b", 0.0);
+    forceField->addParticle(vector<double>());
+    forceField->addParticle(vector<double>());
+    vector<double> table;
+    for (int i = 0; i < xsize; i++)
+        for (int j = 0; j < ysize; j++)
+            for (int k = 0; k < zsize; k++)
+                table.push_back(sin(0.25*i)+cos(0.33*j)+0.12345*k);
+    forceField->addTabulatedFunction("fn", new Discrete3DFunction(xsize, ysize, zsize, table));
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(0, 0, 0);
+    for (int i = 0; i < (int) table.size(); i++) {
+        positions[1] = Vec3((i%xsize)+1, 0, 0);
+        context.setPositions(positions);
+        context.setParameter("a", (i/xsize)%ysize);
+        context.setParameter("b", i/(xsize*ysize));
+        State state = context.getState(State::Forces | State::Energy);
+        const vector<Vec3>& forces = state.getForces();
+        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[0], 1e-6);
+        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], 1e-6);
+        ASSERT_EQUAL_TOL(table[i]+1.0, state.getPotentialEnergy(), 1e-6);
+    }
+}
+
 void testCoulombLennardJones() {
     const int numMolecules = 300;
     const int numParticles = numMolecules*2;
@@ -725,7 +925,12 @@ int main(int argc, char* argv[]) {
         testExclusions();
         testCutoff();
         testPeriodic();
-        testTabulatedFunction();
+        testContinuous1DFunction();
+        testContinuous2DFunction();
+        testContinuous3DFunction();
+        testDiscrete1DFunction();
+        testDiscrete2DFunction();
+        testDiscrete3DFunction();
         testCoulombLennardJones();
         testParallelComputation();
         testSwitchingFunction();

platforms/opencl/include/OpenCLExpressionUtilities.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) 2009-2011 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -28,6 +28,7 @@
  * -------------------------------------------------------------------------- */
 
 #include "OpenCLContext.h"
+#include "openmm/TabulatedFunction.h"
 #include "lepton/CustomFunction.h"
 #include "lepton/ExpressionTreeNode.h"
 #include "lepton/ParsedExpression.h"
@@ -45,75 +46,81 @@ namespace OpenMM {
 
 class OPENMM_EXPORT_OPENCL OpenCLExpressionUtilities {
 public:
-    OpenCLExpressionUtilities(OpenCLContext& context) : context(context) {
-    }
+    OpenCLExpressionUtilities(OpenCLContext& context);
     /**
      * Generate the source code for calculating a set of expressions.
      *
      * @param expressions    the expressions to generate code for (keys are the variables to store the output values in)
      * @param variables      defines the source code to generate for each variable that may appear in the expressions.  Keys are
      *                       variable names, and the values are the code to generate for them.
-     * @param functions      defines the variable name for each tabulated function that may appear in the expressions
+     * @param functions      the tabulated functions that may appear in the expressions
+     * @param functionNames  defines the variable name for each tabulated function that may appear in the expressions
      * @param prefix         a prefix to put in front of temporary variables
-     * @param functionParams the variable name containing the parameters for each tabulated function
      * @param tempType       the type of value to use for temporary variables (defaults to "real")
      */
     std::string createExpressions(const std::map<std::string, Lepton::ParsedExpression>& expressions, const std::map<std::string, std::string>& variables,
-            const std::vector<std::pair<std::string, std::string> >& functions, const std::string& prefix, const std::string& functionParams, const std::string& tempType="real");
+            const std::vector<const TabulatedFunction*>& functions, const std::vector<std::pair<std::string, std::string> >& functionNames,
+            const std::string& prefix, const std::string& tempType="real");
     /**
      * Generate the source code for calculating a set of expressions.
      *
      * @param expressions    the expressions to generate code for (keys are the variables to store the output values in)
      * @param variables      defines the source code to generate for each variable or precomputed sub-expression that may appear in the expressions.
      *                       Each entry is an ExpressionTreeNode, and the code to generate wherever an identical node appears.
-     * @param functions      defines the variable name for each tabulated function that may appear in the expressions
+     * @param functions      the tabulated functions that may appear in the expressions
+     * @param functionNames  defines the variable name for each tabulated function that may appear in the expressions
      * @param prefix         a prefix to put in front of temporary variables
-     * @param functionParams the variable name containing the parameters for each tabulated function
      * @param tempType       the type of value to use for temporary variables (defaults to "float")
      */
     std::string createExpressions(const std::map<std::string, Lepton::ParsedExpression>& expressions, const std::vector<std::pair<Lepton::ExpressionTreeNode, std::string> >& variables,
-            const std::vector<std::pair<std::string, std::string> >& functions, const std::string& prefix, const std::string& functionParams, const std::string& tempType="float");
+            const std::vector<const TabulatedFunction*>& functions, const std::vector<std::pair<std::string, std::string> >& functionNames,
+            const std::string& prefix, const std::string& tempType="float");
     /**
      * Calculate the spline coefficients for a tabulated function that appears in expressions.
      *
-     * @param values         the tabulated values of the function
-     * @param min            the value of the independent variable corresponding to the first element of values
-     * @param max            the value of the independent variable corresponding to the last element of values
+     * @param function   the function for which to compute coefficients
+     * @param width      on output, the number of floats used for each value
      * @return the spline coefficients
      */
-    std::vector<mm_float4> computeFunctionCoefficients(const std::vector<double>& values, double min, double max);
-    class FunctionPlaceholder;
+    std::vector<float> computeFunctionCoefficients(const TabulatedFunction& function, int& width);
+    /**
+     * Get a Lepton::CustomFunction that can be used to represent a TabulatedFunction when parsing expressions.
+     * 
+     * @param function   the function for which to get a placeholder
+     */
+    Lepton::CustomFunction* getFunctionPlaceholder(const TabulatedFunction& function);
 private:
+    class FunctionPlaceholder : public Lepton::CustomFunction {
+        public:
+            FunctionPlaceholder(int numArgs) : numArgs(numArgs) {
+            }
+            int getNumArguments() const {
+                return numArgs;
+            }
+            double evaluate(const double* arguments) const {
+                return 0.0;
+            }
+            double evaluateDerivative(const double* arguments, const int* derivOrder) const {
+                return 0.0;
+            }
+            CustomFunction* clone() const {
+                return new FunctionPlaceholder(numArgs);
+            }
+        private:
+            int numArgs;
+    };
     void processExpression(std::stringstream& out, const Lepton::ExpressionTreeNode& node,
             std::vector<std::pair<Lepton::ExpressionTreeNode, std::string> >& temps,
-            const std::vector<std::pair<std::string, std::string> >& functions, const std::string& prefix, const std::string& functionParams,
-            const std::vector<Lepton::ParsedExpression>& allExpressions, const std::string& tempType);
+            const std::vector<const TabulatedFunction*>& functions, const std::vector<std::pair<std::string, std::string> >& functionNames,
+            const std::string& prefix, const std::vector<std::vector<double> >& functionParams, const std::vector<Lepton::ParsedExpression>& allExpressions, const std::string& tempType);
     std::string getTempName(const Lepton::ExpressionTreeNode& node, const std::vector<std::pair<Lepton::ExpressionTreeNode, std::string> >& temps);
     void findRelatedTabulatedFunctions(const Lepton::ExpressionTreeNode& node, const Lepton::ExpressionTreeNode& searchNode,
-            const Lepton::ExpressionTreeNode*& valueNode, const Lepton::ExpressionTreeNode*& derivNode);
+            std::vector<const Lepton::ExpressionTreeNode*>& nodes);
     void findRelatedPowers(const Lepton::ExpressionTreeNode& node, const Lepton::ExpressionTreeNode& searchNode,
             std::map<int, const Lepton::ExpressionTreeNode*>& powers);
+    std::vector<std::vector<double> > computeFunctionParameters(const std::vector<const TabulatedFunction*>& functions);
     OpenCLContext& context;
-};
-
-/**
- * This class serves as a placeholder for custom functions in expressions.
- */
-
-class OpenCLExpressionUtilities::FunctionPlaceholder : public Lepton::CustomFunction {
-public:
-    int getNumArguments() const {
-        return 1;
-    }
-    double evaluate(const double* arguments) const {
-        return 0.0;
-    }
-    double evaluateDerivative(const double* arguments, const int* derivOrder) const {
-        return 0.0;
-    }
-    CustomFunction* clone() const {
-        return new FunctionPlaceholder();
-    }
+    FunctionPlaceholder fp1, fp2, fp3;
 };
 
 } // namespace OpenMM

platforms/opencl/include/OpenCLKernels.h

@@ -639,7 +639,7 @@ private:
 class OpenCLCalcCustomNonbondedForceKernel : public CalcCustomNonbondedForceKernel {
 public:
     OpenCLCalcCustomNonbondedForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, const System& system) : CalcCustomNonbondedForceKernel(name, platform),
-            cl(cl), params(NULL), globals(NULL), tabulatedFunctionParams(NULL), interactionGroupData(NULL), forceCopy(NULL), system(system), hasInitializedKernel(false) {
+            cl(cl), params(NULL), globals(NULL), interactionGroupData(NULL), forceCopy(NULL), system(system), hasInitializedKernel(false) {
     }
     ~OpenCLCalcCustomNonbondedForceKernel();
     /**
@@ -670,7 +670,6 @@ private:
     OpenCLContext& cl;
     OpenCLParameterSet* params;
     OpenCLArray* globals;
-    OpenCLArray* tabulatedFunctionParams;
     OpenCLArray* interactionGroupData;
     cl::Kernel interactionGroupKernel;
     std::vector<void*> interactionGroupArgs;
@@ -742,7 +741,7 @@ class OpenCLCalcCustomGBForceKernel : public CalcCustomGBForceKernel {
 public:
     OpenCLCalcCustomGBForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, const System& system) : CalcCustomGBForceKernel(name, platform),
             hasInitializedKernels(false), cl(cl), params(NULL), computedValues(NULL), energyDerivs(NULL), energyDerivChain(NULL), longEnergyDerivs(NULL), globals(NULL),
-            valueBuffers(NULL), longValueBuffers(NULL), tabulatedFunctionParams(NULL), system(system) {
+            valueBuffers(NULL), longValueBuffers(NULL), system(system) {
     }
     ~OpenCLCalcCustomGBForceKernel();
     /**
@@ -780,7 +779,6 @@ private:
     OpenCLArray* globals;
     OpenCLArray* valueBuffers;
     OpenCLArray* longValueBuffers;
-    OpenCLArray* tabulatedFunctionParams;
     std::vector<std::string> globalParamNames;
     std::vector<cl_float> globalParamValues;
     std::vector<OpenCLArray*> tabulatedFunctions;
@@ -841,8 +839,7 @@ class OpenCLCalcCustomHbondForceKernel : public CalcCustomHbondForceKernel {
 public:
     OpenCLCalcCustomHbondForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, const System& system) : CalcCustomHbondForceKernel(name, platform),
             hasInitializedKernel(false), cl(cl), donorParams(NULL), acceptorParams(NULL), donors(NULL), acceptors(NULL),
-            donorBufferIndices(NULL), acceptorBufferIndices(NULL), globals(NULL), donorExclusions(NULL), acceptorExclusions(NULL),
-            tabulatedFunctionParams(NULL), system(system) {
+            donorBufferIndices(NULL), acceptorBufferIndices(NULL), globals(NULL), donorExclusions(NULL), acceptorExclusions(NULL), system(system) {
     }
     ~OpenCLCalcCustomHbondForceKernel();
     /**
@@ -881,7 +878,6 @@ private:
     OpenCLArray* acceptorBufferIndices;
     OpenCLArray* donorExclusions;
     OpenCLArray* acceptorExclusions;
-    OpenCLArray* tabulatedFunctionParams;
     std::vector<std::string> globalParamNames;
     std::vector<cl_float> globalParamValues;
     std::vector<OpenCLArray*> tabulatedFunctions;
@@ -895,7 +891,7 @@ private:
 class OpenCLCalcCustomCompoundBondForceKernel : public CalcCustomCompoundBondForceKernel {
 public:
     OpenCLCalcCustomCompoundBondForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, const System& system) : CalcCustomCompoundBondForceKernel(name, platform),
-            cl(cl), params(NULL), globals(NULL), tabulatedFunctionParams(NULL), system(system) {
+            cl(cl), params(NULL), globals(NULL), system(system) {
     }
     ~OpenCLCalcCustomCompoundBondForceKernel();
     /**
@@ -927,7 +923,6 @@ private:
     OpenCLContext& cl;
     OpenCLParameterSet* params;
     OpenCLArray* globals;
-    OpenCLArray* tabulatedFunctionParams;
     std::vector<std::string> globalParamNames;
     std::vector<cl_float> globalParamValues;
     std::vector<OpenCLArray*> tabulatedFunctions;

platforms/opencl/tests/TestOpenCLCustomCompoundBondForce.cpp

@@ -199,6 +199,103 @@ void testParallelComputation() {
         ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
 }
 
+void testContinuous2DFunction() {
+    const int xsize = 10;
+    const int ysize = 11;
+    const double xmin = 0.4;
+    const double xmax = 1.1;
+    const double ymin = 0.0;
+    const double ymax = 0.9;
+    System system;
+    system.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    CustomCompoundBondForce* forceField = new CustomCompoundBondForce(1, "fn(x1,y1)+1");
+    vector<int> particles(1, 0);
+    forceField->addBond(particles, vector<double>());
+    vector<double> table(xsize*ysize);
+    for (int i = 0; i < xsize; i++) {
+        for (int j = 0; j < ysize; j++) {
+            double x = xmin + i*(xmax-xmin)/xsize;
+            double y = ymin + j*(ymax-ymin)/ysize;
+            table[i+xsize*j] = sin(0.25*x)*cos(0.33*y);
+        }
+    }
+    forceField->addTabulatedFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(1);
+    for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
+        for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
+            positions[0] = Vec3(x, y, 1.5);
+            context.setPositions(positions);
+            State state = context.getState(State::Forces | State::Energy);
+            const vector<Vec3>& forces = state.getForces();
+            double energy = 1;
+            Vec3 force(0, 0, 0);
+            if (x >= xmin && x <= xmax && y >= ymin && y <= ymax) {
+                energy = sin(0.25*x)*cos(0.33*y)+1;
+                force[0] = -0.25*cos(0.25*x)*cos(0.33*y);
+                force[1] = 0.3*sin(0.25*x)*sin(0.33*y);
+            }
+            ASSERT_EQUAL_VEC(force, forces[0], 0.1);
+            ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.05);
+        }
+    }
+}
+
+void testContinuous3DFunction() {
+    const int xsize = 10;
+    const int ysize = 11;
+    const int zsize = 12;
+    const double xmin = 0.4;
+    const double xmax = 1.1;
+    const double ymin = 0.0;
+    const double ymax = 0.9;
+    const double zmin = 0.2;
+    const double zmax = 1.3;
+    System system;
+    system.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    CustomCompoundBondForce* forceField = new CustomCompoundBondForce(1, "fn(x1,y1,z1)+1");
+    vector<int> particles(1, 0);
+    forceField->addBond(particles, vector<double>());
+    vector<double> table(xsize*ysize*zsize);
+    for (int i = 0; i < xsize; i++) {
+        for (int j = 0; j < ysize; j++) {
+            for (int k = 0; k < zsize; k++) {
+                double x = xmin + i*(xmax-xmin)/xsize;
+                double y = ymin + j*(ymax-ymin)/ysize;
+                double z = zmin + k*(zmax-zmin)/zsize;
+                table[i+xsize*j+xsize*ysize*k] = sin(0.25*x)*cos(0.33*y)*(1+z);
+            }
+        }
+    }
+    forceField->addTabulatedFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(1);
+    for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
+        for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
+            for (double z = zmin-0.15; z < zmax+0.2; z += 0.1) {
+                positions[0] = Vec3(x, y, z);
+                context.setPositions(positions);
+                State state = context.getState(State::Forces | State::Energy);
+                const vector<Vec3>& forces = state.getForces();
+                double energy = 1;
+                Vec3 force(0, 0, 0);
+                if (x >= xmin && x <= xmax && y >= ymin && y <= ymax && z >= zmin && z <= zmax) {
+                    energy = sin(0.25*x)*cos(0.33*y)*(1.0+z)+1;
+                    force[0] = -0.25*cos(0.25*x)*cos(0.33*y)*(1.0+z);
+                    force[1] = 0.3*sin(0.25*x)*sin(0.33*y)*(1.0+z);
+                    force[2] = -sin(0.25*x)*cos(0.33*y);
+                }
+                ASSERT_EQUAL_VEC(force, forces[0], 0.1);
+                ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.05);
+            }
+        }
+    }
+}
+
 int main(int argc, char* argv[]) {
     try {
         if (argc > 1)
@@ -206,6 +303,8 @@ int main(int argc, char* argv[]) {
         testBond();
         testPositionDependence();
         testParallelComputation();
+        testContinuous2DFunction();
+        testContinuous3DFunction();
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;

platforms/opencl/tests/TestOpenCLCustomGBForce.cpp

@@ -277,7 +277,7 @@ void testTabulatedFunction() {
     vector<double> table;
     for (int i = 0; i < 21; i++)
         table.push_back(std::sin(0.25*i));
-    force->addFunction("fn", table, 1.0, 6.0);
+    force->addTabulatedFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
     system.addForce(force);
     Context context(system, integrator, platform);
     vector<Vec3> positions(2);

platforms/opencl/tests/TestOpenCLCustomHbondForce.cpp

@@ -214,7 +214,7 @@ void testCustomFunctions() {
     vector<double> function(2);
     function[0] = 0;
     function[1] = 1;
-    custom->addFunction("foo", function, 0, 10);
+    custom->addTabulatedFunction("foo", new Continuous1DFunction(function, 0, 10));
     system.addForce(custom);
     Context context(system, integrator, platform);
     vector<Vec3> positions(3);

platforms/reference/tests/TestReferenceCustomGBForce.cpp

@@ -281,7 +281,7 @@ void testTabulatedFunction() {
     vector<double> table;
     for (int i = 0; i < 21; i++)
         table.push_back(std::sin(0.25*i));
-    force->addFunction("fn", table, 1.0, 6.0);
+    force->addTabulatedFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
     system.addForce(force);
     Context context(system, integrator, platform);
     vector<Vec3> positions(2);

platforms/reference/tests/TestReferenceCustomHbondForce.cpp

@@ -217,7 +217,7 @@ void testCustomFunctions() {
     vector<double> function(2);
     function[0] = 0;
     function[1] = 1;
-    custom->addFunction("foo", function, 0, 10);
+    custom->addTabulatedFunction("foo", new Continuous1DFunction(function, 0, 10));
     system.addForce(custom);
     Context context(system, integrator, platform);
     vector<Vec3> positions(3);

serialization/src/CustomCompoundBondForceProxy.cpp

@@ -73,6 +73,9 @@ void CustomCompoundBondForceProxy::serialize(const void* object, SerializationNo
             node.setDoubleProperty(key.str(), params[j]);
         }
     }
+    SerializationNode& functions = node.createChildNode("Functions");
+    for (int i = 0; i < force.getNumTabulatedFunctions(); i++)
+        functions.createChildNode("Function", &force.getTabulatedFunction(i)).setStringProperty("name", force.getTabulatedFunctionName(i));
 }
 
 void* CustomCompoundBondForceProxy::deserialize(const SerializationNode& node) const {
@@ -110,6 +113,22 @@ void* CustomCompoundBondForceProxy::deserialize(const SerializationNode& node) c
             }
             force->addBond(particles, params);
         }
+        const SerializationNode& functions = node.getChildNode("Functions");
+        for (int i = 0; i < (int) functions.getChildren().size(); i++) {
+            const SerializationNode& function = functions.getChildren()[i];
+            if (function.hasProperty("type")) {
+                force->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>());
+            }
+            else {
+                // This is an old file created before TabulatedFunction existed.
+                
+                const SerializationNode& valuesNode = function.getChildNode("Values");
+                vector<double> values;
+                for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
+                    values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
+                force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
+            }
+        }
         return force;
     }
     catch (...) {