Created new API for tabulated functions

openmmapi/include/OpenMM.h

@@ -62,6 +62,7 @@
 #include "openmm/RBTorsionForce.h"
 #include "openmm/State.h"
 #include "openmm/System.h"
+#include "openmm/TabulatedFunction.h"
 #include "openmm/Units.h"
 #include "openmm/VariableLangevinIntegrator.h"
 #include "openmm/VariableVerletIntegrator.h"

openmmapi/include/openmm/CustomCompoundBondForce.h

@@ -32,6 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#include "TabulatedFunction.h"
 #include "Force.h"
 #include "Vec3.h"
 #include <vector>
@@ -91,8 +92,8 @@ namespace OpenMM {
  * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, step, delta.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
  *
- * In addition, you can call addFunction() to define a new function based on tabulated values.  You specify a vector of
- * values, and a natural spline is created from them.  That function can then appear in the expression.
+ * In addition, you can call addFunction() to define a new function based on tabulated values.  You specify the function by
+ * creating a TabulatedFunction object.  That function can then appear in the expression.
  */
 
 class OPENMM_EXPORT CustomCompoundBondForce : public Force {
@@ -229,33 +230,54 @@ public:
      * Add a tabulated function that may appear in the energy expression.
      *
      * @param name           the name of the function as it appears in expressions
-     * @param values         the tabulated values of the function f(x) at uniformly spaced values of x between min and max.
-     *                       The function is assumed to be zero for x &lt; min or x &gt; max.
-     * @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       a TabulatedFunction object defining the function.  The TabulatedFunction
+     *                       should have been created on the heap with the "new" operator.  The
+     *                       Force takes over ownership of it, and deletes it when the Force itself is deleted.
      * @return the index of the function that was added
      */
+    int addFunction(const std::string& name, TabulatedFunction* function);
+    /**
+     * Get a const reference to a tabulated function that may appear in the energy expression.
+     *
+     * @param index     the index of the function to get
+     * @return the TabulatedFunction object defining the function
+     */
+    const TabulatedFunction& getFunction(int index) const;
+    /**
+     * Get a reference to a tabulated function that may appear in the energy expression.
+     *
+     * @param index     the index of the function to get
+     * @return the TabulatedFunction object defining the function
+     */
+    TabulatedFunction& getFunction(int index);
+    /**
+     * Get the name of a tabulated function that may appear in the energy expression.
+     *
+     * @param index     the index of the function to get
+     * @return the name of the function as it appears in expressions
+     */
+    const std::string& getFunctionName(int index);
+    /**
+     * Add a tabulated function that may appear in the energy expression.
+     *
+     * @deprecated This method exists only for backward compatibility.  Use the version that takes
+     * a TabulatedFunction instead.
+     */
     int addFunction(const std::string& name, const std::vector<double>& values, double min, double max);
     /**
      * Get the parameters for a tabulated function that may appear in the energy expression.
      *
-     * @param index          the index of the function for which to get parameters
-     * @param name           the name of the function as it appears in expressions
-     * @param values         the tabulated values of the function f(x) at uniformly spaced values of x between min and max.
-     *                       The function is assumed to be zero for x &lt; min or x &gt; max.
-     * @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
+     * @deprecated This method exists only for backward compatibility.  Use the version that takes
+     * a TabulatedFunction instead.  If the specified function is not a Continuous1DFunction, this throws
+     * an exception.
      */
     void getFunctionParameters(int index, std::string& name, std::vector<double>& values, double& min, double& max) const;
     /**
-     * Set the parameters for a tabulated function that may appear in algebraic expressions.
+     * Set the parameters for a tabulated function that may appear in the energy expression.
      *
-     * @param index          the index of the function for which to set parameters
-     * @param name           the name of the function as it appears in expressions
-     * @param values         the tabulated values of the function f(x) at uniformly spaced values of x between min and max.
-     *                       The function is assumed to be zero for x &lt; min or x &gt; max.
-     * @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
+     * @deprecated This method exists only for backward compatibility.  Use the version that takes
+     * a TabulatedFunction instead.  If the specified function is not a Continuous1DFunction, this throws
+     * an exception.
      */
     void setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double max);
     /**
@@ -333,12 +355,10 @@ public:
 class CustomCompoundBondForce::FunctionInfo {
 public:
     std::string name;
-    std::vector<double> values;
-    double min, max;
+    TabulatedFunction* function;
     FunctionInfo() {
     }
-    FunctionInfo(const std::string& name, const std::vector<double>& values, double min, double max) :
-        name(name), values(values), min(min), max(max) {
+    FunctionInfo(const std::string& name, TabulatedFunction* function) : name(name), function(function) {
     }
 };
 

openmmapi/include/openmm/CustomGBForce.h

@@ -32,6 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#include "TabulatedFunction.h"
 #include "Force.h"
 #include "Vec3.h"
 #include <map>
@@ -134,8 +135,8 @@ namespace OpenMM {
  * have the suffix "1" or "2" appended to them to indicate the values for the two interacting particles.  As seen in the above example,
  * an expression may also involve intermediate quantities that are defined following the main expression, using ";" as a separator.
  *
- * In addition, you can call addFunction() to define a new function based on tabulated values.  You specify a vector of
- * values, and a natural spline is created from them.  That function can then appear in expressions.
+ * In addition, you can call addFunction() to define a new function based on tabulated values.  You specify the function by
+ * creating a TabulatedFunction object.  That function can then appear in expressions.
  */
 
 class OPENMM_EXPORT CustomGBForce : public Force {
@@ -452,36 +453,57 @@ public:
      */
     void setExclusionParticles(int index, int particle1, int particle2);
     /**
-     * Add a tabulated function that may appear in the energy expression.
+     * Add a tabulated function that may appear in expressions.
      *
      * @param name           the name of the function as it appears in expressions
-     * @param values         the tabulated values of the function f(x) at uniformly spaced values of x between min and max.
-     *                       The function is assumed to be zero for x &lt; min or x &gt; max.
-     * @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       a TabulatedFunction object defining the function.  The TabulatedFunction
+     *                       should have been created on the heap with the "new" operator.  The
+     *                       Force takes over ownership of it, and deletes it when the Force itself is deleted.
      * @return the index of the function that was added
      */
+    int addFunction(const std::string& name, TabulatedFunction* function);
+    /**
+     * Get a const reference to a tabulated function that may appear in expressions.
+     *
+     * @param index     the index of the function to get
+     * @return the TabulatedFunction object defining the function
+     */
+    const TabulatedFunction& getFunction(int index) const;
+    /**
+     * Get a reference to a tabulated function that may appear in expressions.
+     *
+     * @param index     the index of the function to get
+     * @return the TabulatedFunction object defining the function
+     */
+    TabulatedFunction& getFunction(int index);
+    /**
+     * Get the name of a tabulated function that may appear in expressions.
+     *
+     * @param index     the index of the function to get
+     * @return the name of the function as it appears in expressions
+     */
+    const std::string& getFunctionName(int index);
+    /**
+     * Add a tabulated function that may appear in expressions.
+     *
+     * @deprecated This method exists only for backward compatibility.  Use the version that takes
+     * a TabulatedFunction instead.
+     */
     int addFunction(const std::string& name, const std::vector<double>& values, double min, double max);
     /**
-     * Get the parameters for a tabulated function that may appear in the energy expression.
+     * Get the parameters for a tabulated function that may appear in expressions.
      *
-     * @param index          the index of the function for which to get parameters
-     * @param name           the name of the function as it appears in expressions
-     * @param values         the tabulated values of the function f(x) at uniformly spaced values of x between min and max.
-     *                       The function is assumed to be zero for x &lt; min or x &gt; max.
-     * @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
+     * @deprecated This method exists only for backward compatibility.  Use the version that takes
+     * a TabulatedFunction instead.  If the specified function is not a Continuous1DFunction, this throws
+     * an exception.
      */
     void getFunctionParameters(int index, std::string& name, std::vector<double>& values, double& min, double& max) const;
     /**
-     * Set the parameters for a tabulated function that may appear in algebraic expressions.
+     * Set the parameters for a tabulated function that may appear in expressions.
      *
-     * @param index          the index of the function for which to set parameters
-     * @param name           the name of the function as it appears in expressions
-     * @param values         the tabulated values of the function f(x) at uniformly spaced values of x between min and max.
-     *                       The function is assumed to be zero for x &lt; min or x &gt; max.
-     * @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
+     * @deprecated This method exists only for backward compatibility.  Use the version that takes
+     * a TabulatedFunction instead.  If the specified function is not a Continuous1DFunction, this throws
+     * an exception.
      */
     void setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double max);
     /**
@@ -577,12 +599,10 @@ public:
 class CustomGBForce::FunctionInfo {
 public:
     std::string name;
-    std::vector<double> values;
-    double min, max;
+    TabulatedFunction* function;
     FunctionInfo() {
     }
-    FunctionInfo(const std::string& name, const std::vector<double>& values, double min, double max) :
-        name(name), values(values), min(min), max(max) {
+    FunctionInfo(const std::string& name, TabulatedFunction* function) : name(name), function(function) {
     }
 };
 

openmmapi/include/openmm/CustomHbondForce.h

@@ -32,6 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#include "TabulatedFunction.h"
 #include "Force.h"
 #include "Vec3.h"
 #include <map>
@@ -91,8 +92,8 @@ namespace OpenMM {
  * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, step, delta.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
  *
- * In addition, you can call addFunction() to define a new function based on tabulated values.  You specify a vector of
- * values, and a natural spline is created from them.  That function can then appear in the expression.
+ * In addition, you can call addFunction() to define a new function based on tabulated values.  You specify the function by
+ * creating a TabulatedFunction object.  That function can then appear in the expression.
  */
 
 class OPENMM_EXPORT CustomHbondForce : public Force {
@@ -374,33 +375,54 @@ public:
      * Add a tabulated function that may appear in the energy expression.
      *
      * @param name           the name of the function as it appears in expressions
-     * @param values         the tabulated values of the function f(x) at uniformly spaced values of x between min and max.
-     *                       The function is assumed to be zero for x &lt; min or x &gt; max.
-     * @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       a TabulatedFunction object defining the function.  The TabulatedFunction
+     *                       should have been created on the heap with the "new" operator.  The
+     *                       Force takes over ownership of it, and deletes it when the Force itself is deleted.
      * @return the index of the function that was added
      */
+    int addFunction(const std::string& name, TabulatedFunction* function);
+    /**
+     * Get a const reference to a tabulated function that may appear in the energy expression.
+     *
+     * @param index     the index of the function to get
+     * @return the TabulatedFunction object defining the function
+     */
+    const TabulatedFunction& getFunction(int index) const;
+    /**
+     * Get a reference to a tabulated function that may appear in the energy expression.
+     *
+     * @param index     the index of the function to get
+     * @return the TabulatedFunction object defining the function
+     */
+    TabulatedFunction& getFunction(int index);
+    /**
+     * Get the name of a tabulated function that may appear in the energy expression.
+     *
+     * @param index     the index of the function to get
+     * @return the name of the function as it appears in expressions
+     */
+    const std::string& getFunctionName(int index);
+    /**
+     * Add a tabulated function that may appear in the energy expression.
+     *
+     * @deprecated This method exists only for backward compatibility.  Use the version that takes
+     * a TabulatedFunction instead.
+     */
     int addFunction(const std::string& name, const std::vector<double>& values, double min, double max);
     /**
      * Get the parameters for a tabulated function that may appear in the energy expression.
      *
-     * @param index          the index of the function for which to get parameters
-     * @param name           the name of the function as it appears in expressions
-     * @param values         the tabulated values of the function f(x) at uniformly spaced values of x between min and max.
-     *                       The function is assumed to be zero for x &lt; min or x &gt; max.
-     * @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
+     * @deprecated This method exists only for backward compatibility.  Use the version that takes
+     * a TabulatedFunction instead.  If the specified function is not a Continuous1DFunction, this throws
+     * an exception.
      */
     void getFunctionParameters(int index, std::string& name, std::vector<double>& values, double& min, double& max) const;
     /**
-     * Set the parameters for a tabulated function that may appear in algebraic expressions.
+     * Set the parameters for a tabulated function that may appear in the energy expression.
      *
-     * @param index          the index of the function for which to set parameters
-     * @param name           the name of the function as it appears in expressions
-     * @param values         the tabulated values of the function f(x) at uniformly spaced values of x between min and max.
-     *                       The function is assumed to be zero for x &lt; min or x &gt; max.
-     * @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
+     * @deprecated This method exists only for backward compatibility.  Use the version that takes
+     * a TabulatedFunction instead.  If the specified function is not a Continuous1DFunction, this throws
+     * an exception.
      */
     void setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double max);
     /**
@@ -499,12 +521,10 @@ public:
 class CustomHbondForce::FunctionInfo {
 public:
     std::string name;
-    std::vector<double> values;
-    double min, max;
+    TabulatedFunction* function;
     FunctionInfo() {
     }
-    FunctionInfo(const std::string& name, const std::vector<double>& values, double min, double max) :
-        name(name), values(values), min(min), max(max) {
+    FunctionInfo(const std::string& name, TabulatedFunction* function) : name(name), function(function) {
     }
 };
 

openmmapi/include/openmm/CustomNonbondedForce.h

@@ -32,6 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#include "TabulatedFunction.h"
 #include "Force.h"
 #include "Vec3.h"
 #include <map>
@@ -124,8 +125,8 @@ namespace OpenMM {
  * have the suffix "1" or "2" appended to them to indicate the values for the two interacting particles.  As seen in the above example,
  * the expression may also involve intermediate quantities that are defined following the main expression, using ";" as a separator.
  *
- * In addition, you can call addFunction() to define a new function based on tabulated values.  You specify a vector of
- * values, and a natural spline is created from them.  That function can then appear in the expression.
+ * In addition, you can call addFunction() to define a new function based on tabulated values.  You specify the function by
+ * creating a TabulatedFunction object.  That function can then appear in the expression.
  */
 
 class OPENMM_EXPORT CustomNonbondedForce : public Force {
@@ -359,33 +360,54 @@ public:
      * Add a tabulated function that may appear in the energy expression.
      *
      * @param name           the name of the function as it appears in expressions
-     * @param values         the tabulated values of the function f(x) at uniformly spaced values of x between min and max.
-     *                       The function is assumed to be zero for x &lt; min or x &gt; max.
-     * @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       a TabulatedFunction object defining the function.  The TabulatedFunction
+     *                       should have been created on the heap with the "new" operator.  The
+     *                       Force takes over ownership of it, and deletes it when the Force itself is deleted.
      * @return the index of the function that was added
      */
+    int addFunction(const std::string& name, TabulatedFunction* function);
+    /**
+     * Get a const reference to a tabulated function that may appear in the energy expression.
+     *
+     * @param index     the index of the function to get
+     * @return the TabulatedFunction object defining the function
+     */
+    const TabulatedFunction& getFunction(int index) const;
+    /**
+     * Get a reference to a tabulated function that may appear in the energy expression.
+     *
+     * @param index     the index of the function to get
+     * @return the TabulatedFunction object defining the function
+     */
+    TabulatedFunction& getFunction(int index);
+    /**
+     * Get the name of a tabulated function that may appear in the energy expression.
+     *
+     * @param index     the index of the function to get
+     * @return the name of the function as it appears in expressions
+     */
+    const std::string& getFunctionName(int index);
+    /**
+     * Add a tabulated function that may appear in the energy expression.
+     *
+     * @deprecated This method exists only for backward compatibility.  Use the version that takes
+     * a TabulatedFunction instead.
+     */
     int addFunction(const std::string& name, const std::vector<double>& values, double min, double max);
     /**
      * Get the parameters for a tabulated function that may appear in the energy expression.
      *
-     * @param index          the index of the function for which to get parameters
-     * @param name           the name of the function as it appears in expressions
-     * @param values         the tabulated values of the function f(x) at uniformly spaced values of x between min and max.
-     *                       The function is assumed to be zero for x &lt; min or x &gt; max.
-     * @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
+     * @deprecated This method exists only for backward compatibility.  Use the version that takes
+     * a TabulatedFunction instead.  If the specified function is not a Continuous1DFunction, this throws
+     * an exception.
      */
     void getFunctionParameters(int index, std::string& name, std::vector<double>& values, double& min, double& max) const;
     /**
-     * Set the parameters for a tabulated function that may appear in algebraic expressions.
+     * Set the parameters for a tabulated function that may appear in the energy expression.
      *
-     * @param index          the index of the function for which to set parameters
-     * @param name           the name of the function as it appears in expressions
-     * @param values         the tabulated values of the function f(x) at uniformly spaced values of x between min and max.
-     *                       The function is assumed to be zero for x &lt; min or x &gt; max.
-     * @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
+     * @deprecated This method exists only for backward compatibility.  Use the version that takes
+     * a TabulatedFunction instead.  If the specified function is not a Continuous1DFunction, this throws
+     * an exception.
      */
     void setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double max);
     /**
@@ -507,12 +529,10 @@ public:
 class CustomNonbondedForce::FunctionInfo {
 public:
     std::string name;
-    std::vector<double> values;
-    double min, max;
+    TabulatedFunction* function;
     FunctionInfo() {
     }
-    FunctionInfo(const std::string& name, const std::vector<double>& values, double min, double max) :
-        name(name), values(values), min(min), max(max) {
+    FunctionInfo(const std::string& name, TabulatedFunction* function) : name(name), function(function) {
     }
 };
 

openmmapi/include/openmm/TabulatedFunction.h

+#ifndef OPENMM_TabulatedFunction_H_
+#define OPENMM_TabulatedFunction_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit 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) 2014 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 "internal/windowsExport.h"
+#include <vector>
+
+namespace OpenMM {
+
+/**
+ * A TabulatedFunction uses a set of tabulated values to define a mathematical function.
+ * It can be used by various custom forces.
+ * 
+ * TabulatedFunction is an abstract class with concrete subclasses for more specific
+ * types of functions.  There are subclasses for:
+ * 
+ * <ul>
+ * <li>1, 2, and 3 dimensional functions.  The dimensionality of a function means
+ * the number of input arguments it takes.</li>
+ * <li>Continuous and discrete functions.  A continuous function is interpolated by
+ * fitting a natural cubic spline to the tabulated values.  A discrete function is
+ * only defined for integer values of its arguments (that is, at the tabulated points),
+ * and does not try to interpolate between them.  Discrete function can be evaluated
+ * more quickly than continuous ones.</li>
+ * </ul>
+ */
+
+class OPENMM_EXPORT TabulatedFunction {
+public:
+    virtual ~TabulatedFunction() {
+    }
+};
+
+/**
+ * This is a TabulatedFunction that computes a continuous one dimensional function.
+ */
+class OPENMM_EXPORT Continuous1DFunction : public TabulatedFunction {
+public:
+    /**
+     * Create a Continuous1DFunction f(x) based on a set of tabulated values.
+     * 
+     * @param values         the tabulated values of the function f(x) at uniformly spaced values of x between min
+     *                       and max.  A natural cubic spline is used to interpolated between the tabulated values.
+     *                       The function is assumed to be zero for x &lt; min or x &gt; max.
+     * @param min            the value of x corresponding to the first element of values
+     * @param max            the value of x corresponding to the last element of values
+     */
+    Continuous1DFunction(const std::vector<double>& values, double min, double max);
+    /**
+     * Get the parameters for the tabulated function.
+     *
+     * @param values         the tabulated values of the function f(x) at uniformly spaced values of x between min
+     *                       and max.  A natural cubic spline is used to interpolated between the tabulated values.
+     *                       The function is assumed to be zero for x &lt; min or x &gt; max.
+     * @param min            the value of x corresponding to the first element of values
+     * @param max            the value of x corresponding to the last element of values
+     */
+    void getFunctionParameters(std::vector<double>& values, double& min, double& max) const;
+    /**
+     * Set the parameters for the tabulated function.
+     *
+     * @param values         the tabulated values of the function f(x) at uniformly spaced values of x between min
+     *                       and max.  A natural cubic spline is used to interpolated between the tabulated values.
+     *                       The function is assumed to be zero for x &lt; min or x &gt; max.
+     * @param min            the value of x corresponding to the first element of values
+     * @param max            the value of x corresponding to the last element of values
+     */
+    void setFunctionParameters(const std::vector<double>& values, double min, double max);
+private:
+    std::vector<double> values;
+    double min, max;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_TabulatedFunction_H_*/

openmmapi/src/CustomCompoundBondForce.cpp

@@ -120,33 +120,47 @@ void CustomCompoundBondForce::setBondParameters(int index, const vector<int>& pa
     bonds[index].parameters = parameters;
 }
 
+int CustomCompoundBondForce::addFunction(const std::string& name, TabulatedFunction* function) {
+    functions.push_back(FunctionInfo(name, function));
+    return functions.size()-1;
+}
+
+const TabulatedFunction& CustomCompoundBondForce::getFunction(int index) const {
+    ASSERT_VALID_INDEX(index, functions);
+    return *functions[index].function;
+}
+
+TabulatedFunction& CustomCompoundBondForce::getFunction(int index) {
+    ASSERT_VALID_INDEX(index, functions);
+    return *functions[index].function;
+}
+
+const string& CustomCompoundBondForce::getFunctionName(int index) {
+    ASSERT_VALID_INDEX(index, functions);
+    return functions[index].name;
+}
+
 int CustomCompoundBondForce::addFunction(const std::string& name, const std::vector<double>& values, double min, double max) {
-    if (max <= min)
-        throw OpenMMException("CustomCompoundBondForce: max <= min for a tabulated function.");
-    if (values.size() < 2)
-        throw OpenMMException("CustomCompoundBondForce: a tabulated function must have at least two points");
-    functions.push_back(FunctionInfo(name, values, min, max));
+    functions.push_back(FunctionInfo(name, new Continuous1DFunction(values, min, max)));
     return functions.size()-1;
 }
 
 void CustomCompoundBondForce::getFunctionParameters(int index, std::string& name, std::vector<double>& values, double& min, double& max) const {
     ASSERT_VALID_INDEX(index, functions);
+    Continuous1DFunction* function = dynamic_cast<Continuous1DFunction*>(functions[index].function);
+    if (function == NULL)
+        throw OpenMMException("CustomCompoundBondForce: function is not a Continuous1DFunction");
     name = functions[index].name;
-    values = functions[index].values;
-    min = functions[index].min;
-    max = functions[index].max;
+    function->getFunctionParameters(values, min, max);
 }
 
 void CustomCompoundBondForce::setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double max) {
-    if (max <= min)
-        throw OpenMMException("CustomCompoundBondForce: max <= min for a tabulated function.");
-    if (values.size() < 2)
-        throw OpenMMException("CustomCompoundBondForce: a tabulated function must have at least two points");
     ASSERT_VALID_INDEX(index, functions);
+    Continuous1DFunction* function = dynamic_cast<Continuous1DFunction*>(functions[index].function);
+    if (function == NULL)
+        throw OpenMMException("CustomCompoundBondForce: function is not a Continuous1DFunction");
     functions[index].name = name;
-    functions[index].values = values;
-    functions[index].min = min;
-    functions[index].max = max;
+    function->setFunctionParameters(values, min, max);
 }
 
 ForceImpl* CustomCompoundBondForce::createImpl() const {

openmmapi/src/CustomGBForce.cpp

@@ -173,33 +173,47 @@ void CustomGBForce::setExclusionParticles(int index, int particle1, int particle
     exclusions[index].particle2 = particle2;
 }
 
+int CustomGBForce::addFunction(const std::string& name, TabulatedFunction* function) {
+    functions.push_back(FunctionInfo(name, function));
+    return functions.size()-1;
+}
+
+const TabulatedFunction& CustomGBForce::getFunction(int index) const {
+    ASSERT_VALID_INDEX(index, functions);
+    return *functions[index].function;
+}
+
+TabulatedFunction& CustomGBForce::getFunction(int index) {
+    ASSERT_VALID_INDEX(index, functions);
+    return *functions[index].function;
+}
+
+const string& CustomGBForce::getFunctionName(int index) {
+    ASSERT_VALID_INDEX(index, functions);
+    return functions[index].name;
+}
+
 int CustomGBForce::addFunction(const std::string& name, const std::vector<double>& values, double min, double max) {
-    if (max <= min)
-        throw OpenMMException("CustomGBForce: max <= min for a tabulated function.");
-    if (values.size() < 2)
-        throw OpenMMException("CustomGBForce: a tabulated function must have at least two points");
-    functions.push_back(FunctionInfo(name, values, min, max));
+    functions.push_back(FunctionInfo(name, new Continuous1DFunction(values, min, max)));
     return functions.size()-1;
 }
 
 void CustomGBForce::getFunctionParameters(int index, std::string& name, std::vector<double>& values, double& min, double& max) const {
     ASSERT_VALID_INDEX(index, functions);
+    Continuous1DFunction* function = dynamic_cast<Continuous1DFunction*>(functions[index].function);
+    if (function == NULL)
+        throw OpenMMException("CustomGBForce: function is not a Continuous1DFunction");
     name = functions[index].name;
-    values = functions[index].values;
-    min = functions[index].min;
-    max = functions[index].max;
+    function->getFunctionParameters(values, min, max);
 }
 
 void CustomGBForce::setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double max) {
-    if (max <= min)
-        throw OpenMMException("CustomGBForce: max <= min for a tabulated function.");
-    if (values.size() < 2)
-        throw OpenMMException("CustomGBForce: a tabulated function must have at least two points");
     ASSERT_VALID_INDEX(index, functions);
+    Continuous1DFunction* function = dynamic_cast<Continuous1DFunction*>(functions[index].function);
+    if (function == NULL)
+        throw OpenMMException("CustomGBForce: function is not a Continuous1DFunction");
     functions[index].name = name;
-    functions[index].values = values;
-    functions[index].min = min;
-    functions[index].max = max;
+    function->setFunctionParameters(values, min, max);
 }
 
 ForceImpl* CustomGBForce::createImpl() const {

openmmapi/src/CustomHbondForce.cpp

@@ -187,33 +187,47 @@ void CustomHbondForce::setExclusionParticles(int index, int donor, int acceptor)
     exclusions[index].acceptor = acceptor;
 }
 
+int CustomHbondForce::addFunction(const std::string& name, TabulatedFunction* function) {
+    functions.push_back(FunctionInfo(name, function));
+    return functions.size()-1;
+}
+
+const TabulatedFunction& CustomHbondForce::getFunction(int index) const {
+    ASSERT_VALID_INDEX(index, functions);
+    return *functions[index].function;
+}
+
+TabulatedFunction& CustomHbondForce::getFunction(int index) {
+    ASSERT_VALID_INDEX(index, functions);
+    return *functions[index].function;
+}
+
+const string& CustomHbondForce::getFunctionName(int index) {
+    ASSERT_VALID_INDEX(index, functions);
+    return functions[index].name;
+}
+
 int CustomHbondForce::addFunction(const std::string& name, const std::vector<double>& values, double min, double max) {
-    if (max <= min)
-        throw OpenMMException("CustomHbondForce: max <= min for a tabulated function.");
-    if (values.size() < 2)
-        throw OpenMMException("CustomHbondForce: a tabulated function must have at least two points");
-    functions.push_back(FunctionInfo(name, values, min, max));
+    functions.push_back(FunctionInfo(name, new Continuous1DFunction(values, min, max)));
     return functions.size()-1;
 }
 
 void CustomHbondForce::getFunctionParameters(int index, std::string& name, std::vector<double>& values, double& min, double& max) const {
     ASSERT_VALID_INDEX(index, functions);
+    Continuous1DFunction* function = dynamic_cast<Continuous1DFunction*>(functions[index].function);
+    if (function == NULL)
+        throw OpenMMException("CustomHbondForce: function is not a Continuous1DFunction");
     name = functions[index].name;
-    values = functions[index].values;
-    min = functions[index].min;
-    max = functions[index].max;
+    function->getFunctionParameters(values, min, max);
 }
 
 void CustomHbondForce::setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double max) {
-    if (max <= min)
-        throw OpenMMException("CustomHbondForce: max <= min for a tabulated function.");
-    if (values.size() < 2)
-        throw OpenMMException("CustomHbondForce: a tabulated function must have at least two points");
     ASSERT_VALID_INDEX(index, functions);
+    Continuous1DFunction* function = dynamic_cast<Continuous1DFunction*>(functions[index].function);
+    if (function == NULL)
+        throw OpenMMException("CustomHbondForce: function is not a Continuous1DFunction");
     functions[index].name = name;
-    functions[index].values = values;
-    functions[index].min = min;
-    functions[index].max = max;
+    function->setFunctionParameters(values, min, max);
 }
 
 ForceImpl* CustomHbondForce::createImpl() const {

openmmapi/src/CustomNonbondedForce.cpp

@@ -169,34 +169,47 @@ void CustomNonbondedForce::setExclusionParticles(int index, int particle1, int p
     exclusions[index].particle1 = particle1;
     exclusions[index].particle2 = particle2;
 }
+int CustomNonbondedForce::addFunction(const std::string& name, TabulatedFunction* function) {
+    functions.push_back(FunctionInfo(name, function));
+    return functions.size()-1;
+}
+
+const TabulatedFunction& CustomNonbondedForce::getFunction(int index) const {
+    ASSERT_VALID_INDEX(index, functions);
+    return *functions[index].function;
+}
+
+TabulatedFunction& CustomNonbondedForce::getFunction(int index) {
+    ASSERT_VALID_INDEX(index, functions);
+    return *functions[index].function;
+}
+
+const string& CustomNonbondedForce::getFunctionName(int index) {
+    ASSERT_VALID_INDEX(index, functions);
+    return functions[index].name;
+}
 
 int CustomNonbondedForce::addFunction(const std::string& name, const std::vector<double>& values, double min, double max) {
-    if (max <= min)
-        throw OpenMMException("CustomNonbondedForce: max <= min for a tabulated function.");
-    if (values.size() < 2)
-        throw OpenMMException("CustomNonbondedForce: a tabulated function must have at least two points");
-    functions.push_back(FunctionInfo(name, values, min, max));
+    functions.push_back(FunctionInfo(name, new Continuous1DFunction(values, min, max)));
     return functions.size()-1;
 }
 
 void CustomNonbondedForce::getFunctionParameters(int index, std::string& name, std::vector<double>& values, double& min, double& max) const {
     ASSERT_VALID_INDEX(index, functions);
+    Continuous1DFunction* function = dynamic_cast<Continuous1DFunction*>(functions[index].function);
+    if (function == NULL)
+        throw OpenMMException("CustomNonbondedForce: function is not a Continuous1DFunction");
     name = functions[index].name;
-    values = functions[index].values;
-    min = functions[index].min;
-    max = functions[index].max;
+    function->getFunctionParameters(values, min, max);
 }
 
 void CustomNonbondedForce::setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double max) {
-    if (max <= min)
-        throw OpenMMException("CustomNonbondedForce: max <= min for a tabulated function.");
-    if (values.size() < 2)
-        throw OpenMMException("CustomNonbondedForce: a tabulated function must have at least two points");
     ASSERT_VALID_INDEX(index, functions);
+    Continuous1DFunction* function = dynamic_cast<Continuous1DFunction*>(functions[index].function);
+    if (function == NULL)
+        throw OpenMMException("CustomNonbondedForce: function is not a Continuous1DFunction");
     functions[index].name = name;
-    functions[index].values = values;
-    functions[index].min = min;
-    functions[index].max = max;
+    function->setFunctionParameters(values, min, max);
 }
 
 int CustomNonbondedForce::addInteractionGroup(const std::set<int>& set1, const std::set<int>& set2) {

openmmapi/src/TabulatedFunction.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit 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) 2014 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 "openmm/TabulatedFunction.h"
+#include "openmm/OpenMMException.h"
+
+using namespace OpenMM;
+using namespace std;
+
+Continuous1DFunction::Continuous1DFunction(const std::vector<double>& values, double min, double max) {
+    if (max <= min)
+        throw OpenMMException("Continuous1DFunction: max <= min for a tabulated function.");
+    if (values.size() < 2)
+        throw OpenMMException("Continuous1DFunction: a tabulated function must have at least two points");
+    this->values = values;
+    this->min = min;
+    this->max = max;
+}
+
+void Continuous1DFunction::getFunctionParameters(std::vector<double>& values, double& min, double& max) const {
+    values = this->values;
+    min = this->min;
+    max = this->max;
+}
+
+void Continuous1DFunction::setFunctionParameters(const std::vector<double>& values, double min, double max) {
+    if (max <= min)
+        throw OpenMMException("Continuous1DFunction: max <= min for a tabulated function.");
+    if (values.size() < 2)
+        throw OpenMMException("Continuous1DFunction: a tabulated function must have at least two points");
+    this->values = values;
+    this->min = min;
+    this->max = max;
+}