Merge branch 'master' of github.com:leeping/openmm

.travis.yml

+language: cpp
+compiler:
+  - clang
+
+before_install:
+  - sudo apt-get update -qq
+  - sudo apt-get install -qq libpcre3 libpcre3-dev gromacs
+  - sudo apt-get install -qq swig doxygen
+  - sudo apt-get install -qq python-numpy python-scipy python-nose
+
+script:
+  - cmake -DCMAKE_INSTALL_PREFIX=~/OpenMM . 
+  - make 
+  - make test 
+  - make install
+  - ls ~/OpenMM/include
+  - export LD_LIBRARY_PATH=~/OpenMM/lib/
+  - export OPENMM_LIB_PATH=~/OpenMM/lib/
+  - export OPENMM_INCLUDE_PATH=~/OpenMM/include/
+  - cd python
+  - sudo -E python setup.py install
+  - cd tests
+  - nosetests -vv

CMakeLists.txt

@@ -87,8 +87,11 @@ IF(WIN32)
     ENDFOREACH(lib)
     LINK_DIRECTORIES("${CMAKE_CURRENT_BINARY_DIR}/${CMAKE_CFG_INTDIR}")
     SET(PTHREADS_LIB pthreadVC2)
+    SET(PTHREADS_LIB_STATIC pthreadVC2_static_mt)
 ELSE(WIN32)
     SET(PTHREADS_LIB pthread)
+    # in linux, even in static builds we link against the dynamic object (since its tied to libc versions)
+    SET(PTHREADS_LIB_STATIC pthread)
 ENDIF(WIN32)
 
 # The build system will set ARCH64 for 64 bit builds, which require

README.md

 ## OpenMM: A High Performance Molecular Dynamics Library
 
+[![Build Status](https://travis-ci.org/SimTk/openmm.png?branch=master)](https://travis-ci.org/SimTk/openmm)
+
 Introduction
 ------------
 

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

@@ -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) 2008-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -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 addTabulatedFunction() 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 {
@@ -106,6 +107,7 @@ public:
      *                      and per-bond parameters
      */
     explicit CustomCompoundBondForce(int numParticles, const std::string& energy);
+    ~CustomCompoundBondForce();
     /**
      * Get the number of particles used to define each bond.
      */
@@ -133,6 +135,14 @@ public:
     /**
      * Get the number of tabulated functions that have been defined.
      */
+    int getNumTabulatedFunctions() const {
+        return functions.size();
+    }
+    /**
+     * Get the number of tabulated functions that have been defined.
+     * 
+     * @deprecated This method exists only for backward compatibility.  Use getNumTabulatedFunctions() instead.
+     */
     int getNumFunctions() const {
         return functions.size();
     }
@@ -229,33 +239,51 @@ 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 addTabulatedFunction(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& getTabulatedFunction(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& getTabulatedFunction(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& getTabulatedFunctionName(int index) const;
+    /**
+     * Add a tabulated function that may appear in the energy expression.
+     *
+     * @deprecated This method exists only for backward compatibility.  Use addTabulatedFunction() 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 getTabulatedFunctionParameters() 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 setTabulatedFunctionParameters() 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 +361,10 @@ 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

@@ -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) 2008-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -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 addTabulatedFunction() 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 {
@@ -181,6 +182,7 @@ public:
      * Create a CustomGBForce.
      */
     CustomGBForce();
+    ~CustomGBForce();
     /**
      * Get the number of particles for which force field parameters have been defined.
      */
@@ -208,6 +210,14 @@ public:
     /**
      * Get the number of tabulated functions that have been defined.
      */
+    int getNumTabulatedFunctions() const {
+        return functions.size();
+    }
+    /**
+     * Get the number of tabulated functions that have been defined.
+     * 
+     * @deprecated This method exists only for backward compatibility.  Use getNumTabulatedFunctions() instead.
+     */
     int getNumFunctions() const {
         return functions.size();
     }
@@ -452,36 +462,54 @@ 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 addTabulatedFunction(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& getTabulatedFunction(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& getTabulatedFunction(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& getTabulatedFunctionName(int index) const;
+    /**
+     * Add a tabulated function that may appear in expressions.
+     *
+     * @deprecated This method exists only for backward compatibility.  Use addTabulatedFunction() 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 getTabulatedFunctionParameters() 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 setTabulatedFunctionParameters() 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 +605,10 @@ 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

@@ -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) 2008-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -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 addTabulatedFunction() 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 {
@@ -124,6 +125,7 @@ public:
      *                  per-acceptor parameters
      */
     explicit CustomHbondForce(const std::string& energy);
+    ~CustomHbondForce();
     /**
      * Get the number of donors for which force field parameters have been defined.
      */
@@ -163,6 +165,14 @@ public:
     /**
      * Get the number of tabulated functions that have been defined.
      */
+    int getNumTabulatedFunctions() const {
+        return functions.size();
+    }
+    /**
+     * Get the number of tabulated functions that have been defined.
+     * 
+     * @deprecated This method exists only for backward compatibility.  Use getNumTabulatedFunctions() instead.
+     */
     int getNumFunctions() const {
         return functions.size();
     }
@@ -374,33 +384,51 @@ 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 addTabulatedFunction(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& getTabulatedFunction(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& getTabulatedFunction(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& getTabulatedFunctionName(int index) const;
+    /**
+     * Add a tabulated function that may appear in the energy expression.
+     *
+     * @deprecated This method exists only for backward compatibility.  Use addTabulatedFunction() 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 getTabulatedFunctionParameters() 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 setTabulatedFunctionParameters() 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 +527,10 @@ 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

@@ -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) 2008-2013 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -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 addTabulatedFunction() 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 {
@@ -156,6 +157,7 @@ public:
      *                  of r, the distance between them, as well as any global and per-particle parameters
      */
     explicit CustomNonbondedForce(const std::string& energy);
+    ~CustomNonbondedForce();
     /**
      * Get the number of particles for which force field parameters have been defined.
      */
@@ -183,6 +185,14 @@ public:
     /**
      * Get the number of tabulated functions that have been defined.
      */
+    int getNumTabulatedFunctions() const {
+        return functions.size();
+    }
+    /**
+     * Get the number of tabulated functions that have been defined.
+     * 
+     * @deprecated This method exists only for backward compatibility.  Use getNumTabulatedFunctions() instead.
+     */
     int getNumFunctions() const {
         return functions.size();
     }
@@ -359,33 +369,51 @@ 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 addTabulatedFunction(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& getTabulatedFunction(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& getTabulatedFunction(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& getTabulatedFunctionName(int index) const;
+    /**
+     * Add a tabulated function that may appear in the energy expression.
+     *
+     * @deprecated This method exists only for backward compatibility.  Use addTabulatedFunction() 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 getTabulatedFunctionParameters() 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 setTabulatedFunctionParameters() 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 +535,10 @@ 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 interpolate 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 interpolate 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 interpolate 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;
+};
+
+/**
+ * This is a TabulatedFunction that computes a continuous two dimensional function.
+ */
+class OPENMM_EXPORT Continuous2DFunction : public TabulatedFunction {
+public:
+    /**
+     * Create a Continuous2DFunction f(x,y) based on a set of tabulated values.
+     * 
+     * @param values     the tabulated values of the function f(x,y) at xsize uniformly spaced values of x between xmin
+     *                   and xmax, and ysize values of y between ymin and ymax.  A natural cubic spline is used to interpolate between the tabulated values.
+     *                   The function is assumed to be zero when x or y is outside its specified range.  The values should be ordered so that
+     *                   values[i+xsize*j] = f(x_i,y_j), where x_i is the i'th uniformly spaced value of x.  This must be of length xsize*ysize.
+     * @param xsize      the number of table elements along the x direction
+     * @param ysize      the number of table elements along the y direction
+     * @param xmin       the value of x corresponding to the first element of values
+     * @param xmax       the value of x corresponding to the last element of values
+     * @param ymin       the value of y corresponding to the first element of values
+     * @param ymax       the value of y corresponding to the last element of values
+     */
+    Continuous2DFunction(int xsize, int ysize, const std::vector<double>& values, double xmin, double xmax, double ymin, double ymax);
+    /**
+     * Get the parameters for the tabulated function.
+     *
+     * @param values     the tabulated values of the function f(x,y) at xsize uniformly spaced values of x between xmin
+     *                   and xmax, and ysize values of y between ymin and ymax.  A natural cubic spline is used to interpolate between the tabulated values.
+     *                   The function is assumed to be zero when x or y is outside its specified range.  The values should be ordered so that
+     *                   values[i+xsize*j] = f(x_i,y_j), where x_i is the i'th uniformly spaced value of x.  This must be of length xsize*ysize.
+     * @param xsize      the number of table elements along the x direction
+     * @param ysize      the number of table elements along the y direction
+     * @param xmin       the value of x corresponding to the first element of values
+     * @param xmax       the value of x corresponding to the last element of values
+     * @param ymin       the value of y corresponding to the first element of values
+     * @param ymax       the value of y corresponding to the last element of values
+     */
+    void getFunctionParameters(int& xsize, int& ysize, std::vector<double>& values, double& xmin, double& xmax, double& ymin, double& ymax) const;
+    /**
+     * Set the parameters for the tabulated function.
+     *
+     * @param values     the tabulated values of the function f(x,y) at xsize uniformly spaced values of x between xmin
+     *                   and xmax, and ysize values of y between ymin and ymax.  A natural cubic spline is used to interpolate between the tabulated values.
+     *                   The function is assumed to be zero when x or y is outside its specified range.  The values should be ordered so that
+     *                   values[i+xsize*j] = f(x_i,y_j), where x_i is the i'th uniformly spaced value of x.  This must be of length xsize*ysize.
+     * @param xsize      the number of table elements along the x direction
+     * @param ysize      the number of table elements along the y direction
+     * @param xmin       the value of x corresponding to the first element of values
+     * @param xmax       the value of x corresponding to the last element of values
+     * @param ymin       the value of y corresponding to the first element of values
+     * @param ymax       the value of y corresponding to the last element of values
+     */
+    void setFunctionParameters(int xsize, int ysize, const std::vector<double>& values, double xmin, double xmax, double ymin, double ymax);
+private:
+    std::vector<double> values;
+    int xsize, ysize;
+    double xmin, xmax, ymin, ymax;
+};
+
+/**
+ * This is a TabulatedFunction that computes a continuous three dimensional function.
+ */
+class OPENMM_EXPORT Continuous3DFunction : public TabulatedFunction {
+public:
+    /**
+     * Create a Continuous3DFunction f(x,y,z) based on a set of tabulated values.
+     * 
+     * @param values     the tabulated values of the function f(x,y,z) at xsize uniformly spaced values of x between xmin
+     *                   and xmax, ysize values of y between ymin and ymax, and zsize values of z between zmin and zmax.
+     *                   A natural cubic spline is used to interpolate between the tabulated values.  The function is
+     *                   assumed to be zero when x, y, or z is outside its specified range.  The values should be ordered so
+     *                   that values[i+xsize*j+xsize*ysize*k] = f(x_i,y_j,z_k), where x_i is the i'th uniformly spaced value of x.
+     *                   This must be of length xsize*ysize*zsize.
+     * @param xsize      the number of table elements along the x direction
+     * @param ysize      the number of table elements along the y direction
+     * @param ysize      the number of table elements along the z direction
+     * @param xmin       the value of x corresponding to the first element of values
+     * @param xmax       the value of x corresponding to the last element of values
+     * @param ymin       the value of y corresponding to the first element of values
+     * @param ymax       the value of y corresponding to the last element of values
+     * @param zmin       the value of z corresponding to the first element of values
+     * @param zmax       the value of z corresponding to the last element of values
+     */
+    Continuous3DFunction(int xsize, int ysize, int zsize, const std::vector<double>& values, double xmin, double xmax, double ymin, double ymax, double zmin, double zmax);
+    /**
+     * Get the parameters for the tabulated function.
+     *
+     * @param values     the tabulated values of the function f(x,y,z) at xsize uniformly spaced values of x between xmin
+     *                   and xmax, ysize values of y between ymin and ymax, and zsize values of z between zmin and zmax.
+     *                   A natural cubic spline is used to interpolate between the tabulated values.  The function is
+     *                   assumed to be zero when x, y, or z is outside its specified range.  The values should be ordered so
+     *                   that values[i+xsize*j+xsize*ysize*k] = f(x_i,y_j,z_k), where x_i is the i'th uniformly spaced value of x.
+     *                   This must be of length xsize*ysize*zsize.
+     * @param xsize      the number of table elements along the x direction
+     * @param ysize      the number of table elements along the y direction
+     * @param ysize      the number of table elements along the z direction
+     * @param xmin       the value of x corresponding to the first element of values
+     * @param xmax       the value of x corresponding to the last element of values
+     * @param ymin       the value of y corresponding to the first element of values
+     * @param ymax       the value of y corresponding to the last element of values
+     * @param zmin       the value of z corresponding to the first element of values
+     * @param zmax       the value of z corresponding to the last element of values
+     */
+    void getFunctionParameters(int& xsize, int& ysize, int& zsize, std::vector<double>& values, double& xmin, double& xmax, double& ymin, double& ymax, double& zmin, double& zmax) const;
+    /**
+     * Set the parameters for the tabulated function.
+     *
+     * @param values     the tabulated values of the function f(x,y,z) at xsize uniformly spaced values of x between xmin
+     *                   and xmax, ysize values of y between ymin and ymax, and zsize values of z between zmin and zmax.
+     *                   A natural cubic spline is used to interpolate between the tabulated values.  The function is
+     *                   assumed to be zero when x, y, or z is outside its specified range.  The values should be ordered so
+     *                   that values[i+xsize*j+xsize*ysize*k] = f(x_i,y_j,z_k), where x_i is the i'th uniformly spaced value of x.
+     *                   This must be of length xsize*ysize*zsize.
+     * @param xsize      the number of table elements along the x direction
+     * @param ysize      the number of table elements along the y direction
+     * @param ysize      the number of table elements along the z direction
+     * @param xmin       the value of x corresponding to the first element of values
+     * @param xmax       the value of x corresponding to the last element of values
+     * @param ymin       the value of y corresponding to the first element of values
+     * @param ymax       the value of y corresponding to the last element of values
+     * @param zmin       the value of z corresponding to the first element of values
+     * @param zmax       the value of z corresponding to the last element of values
+     */
+    void setFunctionParameters(int xsize, int ysize, int zsize, const std::vector<double>& values, double xmin, double xmax, double ymin, double ymax, double zmin, double zmax);
+private:
+    std::vector<double> values;
+    int xsize, ysize, zsize;
+    double xmin, xmax, ymin, ymax, zmin, zmax;
+};
+
+/**
+ * This is a TabulatedFunction that computes a discrete one dimensional function f(x).
+ * To evaluate it, x is rounded to the nearest integer and the table element with that
+ * index is returned.  If the index is outside the range [0, size), the result is undefined.
+ */
+class OPENMM_EXPORT Discrete1DFunction : public TabulatedFunction {
+public:
+    /**
+     * Create a Discrete1DFunction f(x) based on a set of tabulated values.
+     * 
+     * @param values         the tabulated values of the function f(x)
+     */
+    Discrete1DFunction(const std::vector<double>& values);
+    /**
+     * Get the parameters for the tabulated function.
+     *
+     * @param values         the tabulated values of the function f(x)
+     */
+    void getFunctionParameters(std::vector<double>& values) const;
+    /**
+     * Set the parameters for the tabulated function.
+     *
+     * @param values         the tabulated values of the function f(x)
+     */
+    void setFunctionParameters(const std::vector<double>& values);
+private:
+    std::vector<double> values;
+};
+
+/**
+ * This is a TabulatedFunction that computes a discrete two dimensional function f(x,y).
+ * To evaluate it, x and y are each rounded to the nearest integer and the table element with those
+ * indices is returned.  If either index is outside the range [0, size), the result is undefined.
+ */
+class OPENMM_EXPORT Discrete2DFunction : public TabulatedFunction {
+public:
+    /**
+     * Create a Discrete2DFunction f(x,y) based on a set of tabulated values.
+     * 
+     * @param xsize     the number of table elements along the x direction
+     * @param ysize     the number of table elements along the y direction
+     * @param values    the tabulated values of the function f(x,y), ordered so that
+     *                  values[i+xsize*j] = f(i,j).  This must be of length xsize*ysize.
+     */
+    Discrete2DFunction(int xsize, int ysize, const std::vector<double>& values);
+    /**
+     * Get the parameters for the tabulated function.
+     *
+     * @param xsize     the number of table elements along the x direction
+     * @param ysize     the number of table elements along the y direction
+     * @param values    the tabulated values of the function f(x,y), ordered so that
+     *                  values[i+xsize*j] = f(i,j).  This must be of length xsize*ysize.
+     */
+    void getFunctionParameters(int& xsize, int& ysize, std::vector<double>& values) const;
+    /**
+     * Set the parameters for the tabulated function.
+     *
+     * @param xsize     the number of table elements along the x direction
+     * @param ysize     the number of table elements along the y direction
+     * @param values    the tabulated values of the function f(x,y), ordered so that
+     *                  values[i+xsize*j] = f(i,j).  This must be of length xsize*ysize.
+     */
+    void setFunctionParameters(int xsize, int ysize, const std::vector<double>& values);
+private:
+    int xsize, ysize;
+    std::vector<double> values;
+};
+
+/**
+ * This is a TabulatedFunction that computes a discrete three dimensional function f(x,y,z).
+ * To evaluate it, x, y, and z are each rounded to the nearest integer and the table element with those
+ * indices is returned.  If any index is outside the range [0, size), the result is undefined.
+ */
+class OPENMM_EXPORT Discrete3DFunction : public TabulatedFunction {
+public:
+    /**
+     * Create a Discrete3DFunction f(x,y,z) based on a set of tabulated values.
+     * 
+     * @param xsize     the number of table elements along the x direction
+     * @param ysize     the number of table elements along the y direction
+     * @param zsize     the number of table elements along the z direction
+     * @param values    the tabulated values of the function f(x,y,z), ordered so that
+     *                  values[i+xsize*j+xsize*ysize*k] = f(i,j,k).  This must be of length xsize*ysize*zsize.
+     */
+    Discrete3DFunction(int xsize, int ysize, int zsize, const std::vector<double>& values);
+    /**
+     * Get the parameters for the tabulated function.
+     *
+     * @param xsize     the number of table elements along the x direction
+     * @param ysize     the number of table elements along the y direction
+     * @param zsize     the number of table elements along the z direction
+     * @param values    the tabulated values of the function f(x,y,z), ordered so that
+     *                  values[i+xsize*j+xsize*ysize*k] = f(i,j,k).  This must be of length xsize*ysize*zsize.
+     */
+    void getFunctionParameters(int& xsize, int& ysize, int& zsize, std::vector<double>& values) const;
+    /**
+     * Set the parameters for the tabulated function.
+     *
+     * @param xsize     the number of table elements along the x direction
+     * @param ysize     the number of table elements along the y direction
+     * @param zsize     the number of table elements along the z direction
+     * @param values    the tabulated values of the function f(x,y,z), ordered so that
+     *                  values[i+xsize*j+xsize*ysize*k] = f(i,j,k).  This must be of length xsize*ysize*zsize.
+     */
+    void setFunctionParameters(int xsize, int ysize, int zsize, const std::vector<double>& values);
+private:
+    int xsize, ysize, zsize;
+    std::vector<double> values;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_TABULATEDFUNCTION_H_*/

openmmapi/include/openmm/internal/SplineFitter.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -67,7 +67,7 @@ public:
      */
     static void createPeriodicSpline(const std::vector<double>& x, const std::vector<double>& y, std::vector<double>& deriv);
     /**
-     * Evaluate a spline generated by one of the other methods in this class.
+     * Evaluate a 1D spline generated by one of the other methods in this class.
      *
      * @param x     the values of the independent variable at the data points to interpolate
      * @param y     the values of the dependent variable at the data points to interpolate
@@ -77,7 +77,7 @@ public:
      */
     static double evaluateSpline(const std::vector<double>& x, const std::vector<double>& y, const std::vector<double>& deriv, double t);
     /**
-     * Evaluate the derivative of a spline generated by one of the other methods in this class.
+     * Evaluate the derivative of a 1D spline generated by one of the other methods in this class.
      *
      * @param x     the values of the independent variable at the data points to interpolate
      * @param y     the values of the dependent variable at the data points to interpolate
@@ -86,6 +86,90 @@ public:
      * @return the value of the spline's derivative  at the specified point
      */
     static double evaluateSplineDerivative(const std::vector<double>& x, const std::vector<double>& y, const std::vector<double>& deriv, double t);
+    /**
+     * Fit a natural cubic spline surface f(x,y) to a 2D set of data points.  The resulting spline interpolates all the
+     * data points, has a continuous second derivative everywhere, and has a second derivative of 0 at the boundary.
+     *
+     * @param x      the values of the first independent variable at the data points to interpolate.  They must
+     *               be strictly increasing: x[i] > x[i-1].
+     * @param y      the values of the second independent variable at the data points to interpolate.  They must
+     *               be strictly increasing: y[i] > y[i-1].
+     * @param values the values of the dependent variable at the data points to interpolate.  They must be ordered
+     *               so that values[i+xsize*j] = f(x[i],y[j]), where xsize is the length of x.
+     * @param c      on exit, this contains the spline coefficients at each of the data points
+     */
+    static void create2DNaturalSpline(const std::vector<double>& x, const std::vector<double>& y, const std::vector<double>& values, std::vector<std::vector<double> >& c);
+    /**
+     * Evaluate a 2D spline generated by one of the other methods in this class.
+     *
+     * @param x      the values of the first independent variable at the data points to interpolate
+     * @param y      the values of the second independent variable at the data points to interpolate
+     * @param values the values of the dependent variable at the data points to interpolate
+     * @param c      the vector of spline coefficients that was calculated by one of the other methods
+     * @param u      the value of the first independent variable at which to evaluate the spline
+     * @param v      the value of the second independent variable at which to evaluate the spline
+     * @return the value of the spline at the specified point
+     */
+    static double evaluate2DSpline(const std::vector<double>& x, const std::vector<double>& y, const std::vector<double>& values, const std::vector<std::vector<double> >& c, double u, double v);
+    /**
+     * Evaluate the derivatives of a 2D spline generated by one of the other methods in this class.
+     *
+     * @param x      the values of the first independent variable at the data points to interpolate
+     * @param y      the values of the second independent variable at the data points to interpolate
+     * @param values the values of the dependent variable at the data points to interpolate
+     * @param c      the vector of spline coefficients that was calculated by one of the other methods
+     * @param u      the value of the first independent variable at which to evaluate the spline
+     * @param v      the value of the second independent variable at which to evaluate the spline
+     * @param dx     on exit, the x derivative of the spline at the specified point
+     * @param dy     on exit, the y derivative of the spline at the specified point
+     */
+    static void evaluate2DSplineDerivatives(const std::vector<double>& x, const std::vector<double>& y, const std::vector<double>& values, const std::vector<std::vector<double> >& c, double u, double v, double& dx, double& dy);
+    /**
+     * Fit a natural cubic spline surface f(x,y,z) to a 3D set of data points.  The resulting spline interpolates all the
+     * data points, has a continuous second derivative everywhere, and has a second derivative of 0 at the boundary.
+     *
+     * @param x      the values of the first independent variable at the data points to interpolate.  They must
+     *               be strictly increasing: x[i] > x[i-1].
+     * @param y      the values of the second independent variable at the data points to interpolate.  They must
+     *               be strictly increasing: y[i] > y[i-1].
+     * @param z      the values of the third independent variable at the data points to interpolate.  They must
+     *               be strictly increasing: z[i] > z[i-1].
+     * @param values the values of the dependent variable at the data points to interpolate.  They must be ordered
+     *               so that values[i+xsize*j+xsize*ysize*k] = f(x[i],y[j],z[k]), where xsize is the length of x
+     *               and ysize is the length of y.
+     * @param c      on exit, this contains the spline coefficients at each of the data points
+     */
+    static void create3DNaturalSpline(const std::vector<double>& x, const std::vector<double>& y, const std::vector<double>& z, const std::vector<double>& values, std::vector<std::vector<double> >& c);
+    /**
+     * Evaluate a 3D spline generated by one of the other methods in this class.
+     *
+     * @param x      the values of the first independent variable at the data points to interpolate
+     * @param y      the values of the second independent variable at the data points to interpolate
+     * @param z      the values of the third independent variable at the data points to interpolate
+     * @param values the values of the dependent variable at the data points to interpolate
+     * @param c      the vector of spline coefficients that was calculated by one of the other methods
+     * @param u      the value of the first independent variable at which to evaluate the spline
+     * @param v      the value of the second independent variable at which to evaluate the spline
+     * @param w      the value of the third independent variable at which to evaluate the spline
+     * @return the value of the spline at the specified point
+     */
+    static double evaluate3DSpline(const std::vector<double>& x, const std::vector<double>& y, const std::vector<double>& z, const std::vector<double>& values, const std::vector<std::vector<double> >& c, double u, double v, double w);
+    /**
+     * Evaluate the derivatives of a 3D spline generated by one of the other methods in this class.
+     *
+     * @param x      the values of the first independent variable at the data points to interpolate
+     * @param y      the values of the second independent variable at the data points to interpolate
+     * @param z      the values of the third independent variable at the data points to interpolate
+     * @param values the values of the dependent variable at the data points to interpolate
+     * @param c      the vector of spline coefficients that was calculated by one of the other methods
+     * @param u      the value of the first independent variable at which to evaluate the spline
+     * @param v      the value of the second independent variable at which to evaluate the spline
+     * @param w      the value of the third independent variable at which to evaluate the spline
+     * @param dx     on exit, the x derivative of the spline at the specified point
+     * @param dy     on exit, the y derivative of the spline at the specified point
+     * @param dz     on exit, the z derivative of the spline at the specified point
+     */
+    static void evaluate3DSplineDerivatives(const std::vector<double>& x, const std::vector<double>& y, const std::vector<double>& z, const std::vector<double>& values, const std::vector<std::vector<double> >& c, double u, double v, double w, double& dx, double& dy, double &dz);
 private:
     static void solveTridiagonalMatrix(const std::vector<double>& a, const std::vector<double>& b, const std::vector<double>& c, const std::vector<double>& rhs, std::vector<double>& sol);
 };

openmmapi/src/CustomCompoundBondForce.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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -51,6 +51,12 @@ using std::vector;
 CustomCompoundBondForce::CustomCompoundBondForce(int numParticles, const string& energy) : particlesPerBond(numParticles), energyExpression(energy) {
 }
 
+
+CustomCompoundBondForce::~CustomCompoundBondForce() {
+    for (int i = 0; i < (int) functions.size(); i++)
+        delete functions[i].function;
+}
+
 const string& CustomCompoundBondForce::getEnergyFunction() const {
     return energyExpression;
 }
@@ -120,33 +126,47 @@ void CustomCompoundBondForce::setBondParameters(int index, const vector<int>& pa
     bonds[index].parameters = parameters;
 }
 
+int CustomCompoundBondForce::addTabulatedFunction(const std::string& name, TabulatedFunction* function) {
+    functions.push_back(FunctionInfo(name, function));
+    return functions.size()-1;
+}
+
+const TabulatedFunction& CustomCompoundBondForce::getTabulatedFunction(int index) const {
+    ASSERT_VALID_INDEX(index, functions);
+    return *functions[index].function;
+}
+
+TabulatedFunction& CustomCompoundBondForce::getTabulatedFunction(int index) {
+    ASSERT_VALID_INDEX(index, functions);
+    return *functions[index].function;
+}
+
+const string& CustomCompoundBondForce::getTabulatedFunctionName(int index) const {
+    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/CustomCompoundBondForceImpl.cpp

@@ -147,7 +147,7 @@ ParsedExpression CustomCompoundBondForceImpl::prepareExpression(const CustomComp
 ExpressionTreeNode CustomCompoundBondForceImpl::replaceFunctions(const ExpressionTreeNode& node, map<string, int> atoms,
         map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals) {
     const Operation& op = node.getOperation();
-    if (op.getId() != Operation::CUSTOM || op.getNumArguments() < 2)
+    if (op.getId() != Operation::CUSTOM || (op.getName() != "distance" && op.getName() != "angle" && op.getName() != "dihedral"))
     {
         // This is not an angle or dihedral, so process its children.
 

openmmapi/src/CustomGBForce.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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -50,6 +50,11 @@ using std::vector;
 CustomGBForce::CustomGBForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0) {
 }
 
+CustomGBForce::~CustomGBForce() {
+    for (int i = 0; i < (int) functions.size(); i++)
+        delete functions[i].function;
+}
+
 CustomGBForce::NonbondedMethod CustomGBForce::getNonbondedMethod() const {
     return nonbondedMethod;
 }
@@ -173,33 +178,47 @@ void CustomGBForce::setExclusionParticles(int index, int particle1, int particle
     exclusions[index].particle2 = particle2;
 }
 
+int CustomGBForce::addTabulatedFunction(const std::string& name, TabulatedFunction* function) {
+    functions.push_back(FunctionInfo(name, function));
+    return functions.size()-1;
+}
+
+const TabulatedFunction& CustomGBForce::getTabulatedFunction(int index) const {
+    ASSERT_VALID_INDEX(index, functions);
+    return *functions[index].function;
+}
+
+TabulatedFunction& CustomGBForce::getTabulatedFunction(int index) {
+    ASSERT_VALID_INDEX(index, functions);
+    return *functions[index].function;
+}
+
+const string& CustomGBForce::getTabulatedFunctionName(int index) const {
+    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

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -50,6 +50,12 @@ using std::vector;
 CustomHbondForce::CustomHbondForce(const string& energy) : energyExpression(energy), nonbondedMethod(NoCutoff), cutoffDistance(1.0) {
 }
 
+
+CustomHbondForce::~CustomHbondForce() {
+    for (int i = 0; i < (int) functions.size(); i++)
+        delete functions[i].function;
+}
+
 const string& CustomHbondForce::getEnergyFunction() const {
     return energyExpression;
 }
@@ -187,33 +193,47 @@ void CustomHbondForce::setExclusionParticles(int index, int donor, int acceptor)
     exclusions[index].acceptor = acceptor;
 }
 
+int CustomHbondForce::addTabulatedFunction(const std::string& name, TabulatedFunction* function) {
+    functions.push_back(FunctionInfo(name, function));
+    return functions.size()-1;
+}
+
+const TabulatedFunction& CustomHbondForce::getTabulatedFunction(int index) const {
+    ASSERT_VALID_INDEX(index, functions);
+    return *functions[index].function;
+}
+
+TabulatedFunction& CustomHbondForce::getTabulatedFunction(int index) {
+    ASSERT_VALID_INDEX(index, functions);
+    return *functions[index].function;
+}
+
+const string& CustomHbondForce::getTabulatedFunctionName(int index) const {
+    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

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -51,6 +51,11 @@ CustomNonbondedForce::CustomNonbondedForce(const string& energy) : energyExpress
     switchingDistance(-1.0), useSwitchingFunction(false), useLongRangeCorrection(false) {
 }
 
+CustomNonbondedForce::~CustomNonbondedForce() {
+    for (int i = 0; i < (int) functions.size(); i++)
+        delete functions[i].function;
+}
+
 const string& CustomNonbondedForce::getEnergyFunction() const {
     return energyExpression;
 }
@@ -169,34 +174,47 @@ void CustomNonbondedForce::setExclusionParticles(int index, int particle1, int p
     exclusions[index].particle1 = particle1;
     exclusions[index].particle2 = particle2;
 }
+int CustomNonbondedForce::addTabulatedFunction(const std::string& name, TabulatedFunction* function) {
+    functions.push_back(FunctionInfo(name, function));
+    return functions.size()-1;
+}
+
+const TabulatedFunction& CustomNonbondedForce::getTabulatedFunction(int index) const {
+    ASSERT_VALID_INDEX(index, functions);
+    return *functions[index].function;
+}
+
+TabulatedFunction& CustomNonbondedForce::getTabulatedFunction(int index) {
+    ASSERT_VALID_INDEX(index, functions);
+    return *functions[index].function;
+}
+
+const string& CustomNonbondedForce::getTabulatedFunctionName(int index) const {
+    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/SplineFitter.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -190,3 +190,535 @@ void SplineFitter::solveTridiagonalMatrix(const vector<double>& a, const vector<
     for (int i = n-2; i >= 0; i--)
         sol[i] -= gamma[i+1]*sol[i+1];
 }
+
+void SplineFitter::create2DNaturalSpline(const vector<double>& x, const vector<double>& y, const vector<double>& values, vector<vector<double> >& c) {
+    int xsize = x.size(), ysize = y.size();
+    if (xsize < 2 || ysize < 2)
+        throw OpenMMException("create2DNaturalSpline: must have at least two points along each axis");
+    if (values.size() != xsize*ysize)
+        throw OpenMMException("create2DNaturalSpline: incorrect number of values");
+    vector<double> d1(xsize*ysize), d2(xsize*ysize), d12(xsize*ysize);
+    vector<double> t(xsize), deriv(xsize);
+
+    // Compute derivatives with respect to x.
+
+    for (int i = 0; i < ysize; i++) {
+        for (int j = 0; j < xsize; j++)
+            t[j] = values[j+xsize*i];
+        SplineFitter::createNaturalSpline(x, t, deriv);
+        for (int j = 0; j < xsize; j++)
+            d1[j+xsize*i] = SplineFitter::evaluateSplineDerivative(x, t, deriv, x[j]);
+    }
+
+    // Compute derivatives with respect to y.
+
+    t.resize(ysize);
+    deriv.resize(ysize);
+    for (int i = 0; i < xsize; i++) {
+        for (int j = 0; j < ysize; j++)
+            t[j] = values[i+xsize*j];
+        SplineFitter::createNaturalSpline(y, t, deriv);
+        for (int j = 0; j < ysize; j++)
+            d2[i+xsize*j] = SplineFitter::evaluateSplineDerivative(y, t, deriv, y[j]);
+    }
+
+    // Compute cross derivatives.
+
+    t.resize(xsize);
+    deriv.resize(xsize);
+    for (int i = 0; i < ysize; i++) {
+        for (int j = 0; j < xsize; j++)
+            t[j] = d2[j+xsize*i];
+        SplineFitter::createNaturalSpline(x, t, deriv);
+        for (int j = 0; j < xsize; j++)
+            d12[j+xsize*i] = SplineFitter::evaluateSplineDerivative(x, t, deriv, x[j]);
+    }
+
+    // Now compute the coefficients.
+
+    const int wt[] = {
+        1, 0, -3, 2, 0, 0, 0, 0, -3, 0, 9, -6, 2, 0, -6, 4,
+        0, 0, 0, 0, 0, 0, 0, 0, 3, 0, -9, 6, -2, 0, 6, -4,
+        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, -6, 0, 0, -6, 4,
+        0, 0, 3, -2, 0, 0, 0, 0, 0, 0, -9, 6, 0, 0, 6, -4,
+        0, 0, 0, 0, 1, 0, -3, 2, -2, 0, 6, -4, 1, 0, -3, 2,
+        0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 3, -2, 1, 0, -3, 2,
+        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, 2, 0, 0, 3, -2,
+        0, 0, 0, 0, 0, 0, 3, -2, 0, 0, -6, 4, 0, 0, 3, -2,
+        0, 1, -2, 1, 0, 0, 0, 0, 0, -3, 6, -3, 0, 2, -4, 2,
+        0, 0, 0, 0, 0, 0, 0, 0, 0, 3, -6, 3, 0, -2, 4, -2,
+        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, 3, 0, 0, 2, -2,
+        0, 0, -1, 1, 0, 0, 0, 0, 0, 0, 3, -3, 0, 0, -2, 2,
+        0, 0, 0, 0, 0, 1, -2, 1, 0, -2, 4, -2, 0, 1, -2, 1,
+        0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 2, -1, 0, 1, -2, 1,
+        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, -1, 0, 0, -1, 1,
+        0, 0, 0, 0, 0, 0, -1, 1, 0, 0, 2, -2, 0, 0, -1, 1
+    };
+    vector<double> rhs(16);
+    c.resize((xsize-1)*(ysize-1));
+    for (int i = 0; i < xsize-1; i++) {
+        for (int j = 0; j < ysize-1; j++) {
+            // Compute the 16 coefficients for patch (i, j).
+
+            int nexti = i+1;
+            int nextj = j+1;
+            double deltax = x[nexti]-x[i];
+            double deltay = y[nextj]-y[j];
+            double e[] = {values[i+j*xsize], values[nexti+j*xsize], values[nexti+nextj*xsize], values[i+nextj*xsize]};
+            double e1[] = {d1[i+j*xsize], d1[nexti+j*xsize], d1[nexti+nextj*xsize], d1[i+nextj*xsize]};
+            double e2[] = {d2[i+j*xsize], d2[nexti+j*xsize], d2[nexti+nextj*xsize], d2[i+nextj*xsize]};
+            double e12[] = {d12[i+j*xsize], d12[nexti+j*xsize], d12[nexti+nextj*xsize], d12[i+nextj*xsize]};
+
+            for (int k = 0; k < 4; k++) {
+                rhs[k] = e[k];
+                rhs[k+4] = e1[k]*deltax;
+                rhs[k+8] = e2[k]*deltay;
+                rhs[k+12] = e12[k]*deltax*deltay;
+            }
+            vector<double>& coeff = c[i+j*(xsize-1)];
+            coeff.resize(16);
+            for (int k = 0; k < 16; k++) {
+                double sum = 0.0;
+                for (int m = 0; m < 16; m++)
+                    sum += wt[k+16*m]*rhs[m];
+                coeff[k] = sum;
+            }
+        }
+    }
+}
+
+double SplineFitter::evaluate2DSpline(const vector<double>& x, const vector<double>& y, const vector<double>& values, const vector<vector<double> >& c, double u, double v) {
+    int xsize = x.size();
+    int ysize = y.size();
+    if (u < x[0] || u > x[xsize-1] || v < y[0] || v > y[ysize-1])
+        throw OpenMMException("evaluate2DSpline: specified point is outside the range defined by the spline");
+
+    // Perform a binary search to identify the interval containing the point to evaluate.
+
+    int lowerx = 0;
+    int upperx = xsize-1;
+    while (upperx-lowerx > 1) {
+        int middle = (upperx+lowerx)/2;
+        if (x[middle] > u)
+            upperx = middle;
+        else
+            lowerx = middle;
+    }
+    int lowery = 0;
+    int uppery = ysize-1;
+    while (uppery-lowery > 1) {
+        int middle = (uppery+lowery)/2;
+        if (y[middle] > v)
+            uppery = middle;
+        else
+            lowery = middle;
+    }
+    double deltax = x[upperx]-x[lowerx];
+    double deltay = y[uppery]-y[lowery];
+    double da = (u-x[lowerx])/deltax;
+    double db = (v-y[lowery])/deltay;
+    const vector<double>& coeff = c[lowerx+(xsize-1)*lowery];
+
+    // Evaluate the spline to determine the value.
+
+    double value = 0;
+    for (int i = 3; i >= 0; i--)
+        value = da*value + ((coeff[i*4+3]*db + coeff[i*4+2])*db + coeff[i*4+1])*db + coeff[i*4+0];
+    return value;
+}
+
+void SplineFitter::evaluate2DSplineDerivatives(const vector<double>& x, const vector<double>& y, const vector<double>& values, const vector<vector<double> >& c, double u, double v, double& dx, double &dy) {
+    int xsize = x.size();
+    int ysize = y.size();
+    if (u < x[0] || u > x[xsize-1] || v < y[0] || v > y[ysize-1])
+        throw OpenMMException("evaluate2DSplineDerivatives: specified point is outside the range defined by the spline");
+
+    // Perform a binary search to identify the interval containing the point to evaluate.
+
+    int lowerx = 0;
+    int upperx = xsize-1;
+    while (upperx-lowerx > 1) {
+        int middle = (upperx+lowerx)/2;
+        if (x[middle] > u)
+            upperx = middle;
+        else
+            lowerx = middle;
+    }
+    int lowery = 0;
+    int uppery = ysize-1;
+    while (uppery-lowery > 1) {
+        int middle = (uppery+lowery)/2;
+        if (y[middle] > v)
+            uppery = middle;
+        else
+            lowery = middle;
+    }
+    double deltax = x[upperx]-x[lowerx];
+    double deltay = y[uppery]-y[lowery];
+    double da = (u-x[lowerx])/deltax;
+    double db = (v-y[lowery])/deltay;
+    const vector<double>& coeff = c[lowerx+(xsize-1)*lowery];
+
+    // Evaluate the spline to determine the derivatives.
+
+    dx = 0;
+    dy = 0;
+    for (int i = 3; i >= 0; i--) {
+        dx = db*dx + (3.0*coeff[i+3*4]*da + 2.0*coeff[i+2*4])*da + coeff[i+1*4];
+        dy = da*dy + (3.0*coeff[i*4+3]*db + 2.0*coeff[i*4+2])*db + coeff[i*4+1];
+    }
+    dx /= deltax;
+    dy /= deltay;
+}
+
+void SplineFitter::create3DNaturalSpline(const vector<double>& x, const vector<double>& y, const vector<double>& z, const vector<double>& values, vector<vector<double> >& c) {
+    int xsize = x.size(), ysize = y.size(), zsize = z.size();
+    int xysize = xsize*ysize;
+    if (xsize < 2 || ysize < 2 || zsize < 2)
+        throw OpenMMException("create2DNaturalSpline: must have at least two points along each axis");
+    if (values.size() != xsize*ysize*zsize)
+        throw OpenMMException("create2DNaturalSpline: incorrect number of values");
+    vector<double> d1(xsize*ysize*zsize), d2(xsize*ysize*zsize), d3(xsize*ysize*zsize);
+    vector<double> d12(xsize*ysize*zsize), d13(xsize*ysize*zsize), d23(xsize*ysize*zsize), d123(xsize*ysize*zsize);
+    vector<double> t(xsize), deriv(xsize);
+
+    // Compute derivatives with respect to x.
+
+    for (int i = 0; i < ysize; i++) {
+        for (int j = 0; j < zsize; j++) {
+            for (int k = 0; k < xsize; k++)
+                t[k] = values[k+xsize*i+xysize*j];
+            SplineFitter::createNaturalSpline(x, t, deriv);
+            for (int k = 0; k < xsize; k++)
+                d1[k+xsize*i+xysize*j] = SplineFitter::evaluateSplineDerivative(x, t, deriv, x[k]);
+        }
+    }
+
+    // Compute derivatives with respect to y.
+
+    t.resize(ysize);
+    deriv.resize(ysize);
+    for (int i = 0; i < xsize; i++) {
+        for (int j = 0; j < zsize; j++) {
+            for (int k = 0; k < ysize; k++)
+                t[k] = values[i+xsize*k+xysize*j];
+            SplineFitter::createNaturalSpline(y, t, deriv);
+            for (int k = 0; k < ysize; k++)
+                d2[i+xsize*k+xysize*j] = SplineFitter::evaluateSplineDerivative(y, t, deriv, y[k]);
+        }
+    }
+
+    // Compute derivatives with respect to z.
+
+    t.resize(zsize);
+    deriv.resize(zsize);
+    for (int i = 0; i < xsize; i++) {
+        for (int j = 0; j < ysize; j++) {
+            for (int k = 0; k < zsize; k++)
+                t[k] = values[i+xsize*j+xysize*k];
+            SplineFitter::createNaturalSpline(z, t, deriv);
+            for (int k = 0; k < zsize; k++)
+                d3[i+xsize*j+xysize*k] = SplineFitter::evaluateSplineDerivative(z, t, deriv, z[k]);
+        }
+    }
+
+    // Compute second derivatives with respect to x and y.
+
+    t.resize(xsize);
+    deriv.resize(xsize);
+    for (int i = 0; i < ysize; i++) {
+        for (int j = 0; j < zsize; j++) {
+            for (int k = 0; k < xsize; k++)
+                t[k] = d2[k+xsize*i+xysize*j];
+            SplineFitter::createNaturalSpline(x, t, deriv);
+            for (int k = 0; k < xsize; k++)
+                d12[k+xsize*i+xysize*j] = SplineFitter::evaluateSplineDerivative(x, t, deriv, x[k]);
+        }
+    }
+
+    // Compute second derivatives with respect to y and z.
+
+    t.resize(ysize);
+    deriv.resize(ysize);
+    for (int i = 0; i < zsize; i++) {
+        for (int j = 0; j < xsize; j++) {
+            for (int k = 0; k < ysize; k++)
+                t[k] = d3[j+xsize*k+xysize*i];
+            SplineFitter::createNaturalSpline(y, t, deriv);
+            for (int k = 0; k < ysize; k++)
+                d23[j+xsize*k+xysize*i] = SplineFitter::evaluateSplineDerivative(y, t, deriv, y[k]);
+        }
+    }
+
+    // Compute second derivatives with respect to x and z.
+
+    t.resize(zsize);
+    deriv.resize(zsize);
+    for (int i = 0; i < xsize; i++) {
+        for (int j = 0; j < ysize; j++) {
+            for (int k = 0; k < zsize; k++)
+                t[k] = d1[i+xsize*j+xysize*k];
+            SplineFitter::createNaturalSpline(z, t, deriv);
+            for (int k = 0; k < zsize; k++)
+                d13[i+xsize*j+xysize*k] = SplineFitter::evaluateSplineDerivative(z, t, deriv, z[k]);
+        }
+    }
+
+    // Compute third derivatives with respect to x, y, and z.
+
+    t.resize(xsize);
+    deriv.resize(xsize);
+    for (int i = 0; i < ysize; i++) {
+        for (int j = 0; j < zsize; j++) {
+            for (int k = 0; k < xsize; k++)
+                t[k] = d23[k+xsize*i+xysize*j];
+            SplineFitter::createNaturalSpline(x, t, deriv);
+            for (int k = 0; k < xsize; k++)
+                d123[k+xsize*i+xysize*j] = SplineFitter::evaluateSplineDerivative(x, t, deriv, x[k]);
+        }
+    }
+
+    // Now compute the coefficients.  This involves multiplying by a sparse 64x64 matrix, given
+    // here in packed form.
+
+    const int wt[] = {
+        1,0,1,
+        1,8,1,
+        4,0,-3,1,3,8,-2,9,-1,
+        4,0,2,1,-2,8,1,9,1,
+        1,16,1,
+        1,32,1,
+        4,16,-3,17,3,32,-2,33,-1,
+        4,16,2,17,-2,32,1,33,1,
+        4,0,-3,2,3,16,-2,18,-1,
+        4,8,-3,10,3,32,-2,34,-1,
+        16,0,9,1,-9,2,-9,3,9,8,6,9,3,10,-6,11,-3,16,6,17,-6,18,3,19,-3,32,4,33,2,34,2,35,1,
+        16,0,-6,1,6,2,6,3,-6,8,-3,9,-3,10,3,11,3,16,-4,17,4,18,-2,19,2,32,-2,33,-2,34,-1,35,-1,
+        4,0,2,2,-2,16,1,18,1,
+        4,8,2,10,-2,32,1,34,1,
+        16,0,-6,1,6,2,6,3,-6,8,-4,9,-2,10,4,11,2,16,-3,17,3,18,-3,19,3,32,-2,33,-1,34,-2,35,-1,
+        16,0,4,1,-4,2,-4,3,4,8,2,9,2,10,-2,11,-2,16,2,17,-2,18,2,19,-2,32,1,33,1,34,1,35,1,
+        1,24,1,
+        1,40,1,
+        4,24,-3,25,3,40,-2,41,-1,
+        4,24,2,25,-2,40,1,41,1,
+        1,48,1,
+        1,56,1,
+        4,48,-3,49,3,56,-2,57,-1,
+        4,48,2,49,-2,56,1,57,1,
+        4,24,-3,26,3,48,-2,50,-1,
+        4,40,-3,42,3,56,-2,58,-1,
+        16,24,9,25,-9,26,-9,27,9,40,6,41,3,42,-6,43,-3,48,6,49,-6,50,3,51,-3,56,4,57,2,58,2,59,1,
+        16,24,-6,25,6,26,6,27,-6,40,-3,41,-3,42,3,43,3,48,-4,49,4,50,-2,51,2,56,-2,57,-2,58,-1,59,-1,
+        4,24,2,26,-2,48,1,50,1,
+        4,40,2,42,-2,56,1,58,1,
+        16,24,-6,25,6,26,6,27,-6,40,-4,41,-2,42,4,43,2,48,-3,49,3,50,-3,51,3,56,-2,57,-1,58,-2,59,-1,
+        16,24,4,25,-4,26,-4,27,4,40,2,41,2,42,-2,43,-2,48,2,49,-2,50,2,51,-2,56,1,57,1,58,1,59,1,
+        4,0,-3,4,3,24,-2,28,-1,
+        4,8,-3,12,3,40,-2,44,-1,
+        16,0,9,1,-9,4,-9,5,9,8,6,9,3,12,-6,13,-3,24,6,25,-6,28,3,29,-3,40,4,41,2,44,2,45,1,
+        16,0,-6,1,6,4,6,5,-6,8,-3,9,-3,12,3,13,3,24,-4,25,4,28,-2,29,2,40,-2,41,-2,44,-1,45,-1,
+        4,16,-3,20,3,48,-2,52,-1,
+        4,32,-3,36,3,56,-2,60,-1,
+        16,16,9,17,-9,20,-9,21,9,32,6,33,3,36,-6,37,-3,48,6,49,-6,52,3,53,-3,56,4,57,2,60,2,61,1,
+        16,16,-6,17,6,20,6,21,-6,32,-3,33,-3,36,3,37,3,48,-4,49,4,52,-2,53,2,56,-2,57,-2,60,-1,61,-1,
+        16,0,9,2,-9,4,-9,6,9,16,6,18,3,20,-6,22,-3,24,6,26,-6,28,3,30,-3,48,4,50,2,52,2,54,1,
+        16,8,9,10,-9,12,-9,14,9,32,6,34,3,36,-6,38,-3,40,6,42,-6,44,3,46,-3,56,4,58,2,60,2,62,1,
+        64,0,-27,1,27,2,27,3,-27,4,27,5,-27,6,-27,7,27,8,-18,9,-9,10,18,11,9,12,18,13,9,14,-18,15,-9,16,-18,17,18,18,-9,19,9,20,18,21,-18,22,9,23,-9,24,-18,25,18,26,18,27,-18,28,-9,29,9,30,9,31,-9,32,-12,33,-6,34,-6,35,-3,36,12,37,6,38,6,39,3,40,-12,41,-6,42,12,43,6,44,-6,45,-3,46,6,47,3,48,-12,49,12,50,-6,51,6,52,-6,53,6,54,-3,55,3,56,-8,57,-4,58,-4,59,-2,60,-4,61,-2,62,-2,63,-1,
+        64,0,18,1,-18,2,-18,3,18,4,-18,5,18,6,18,7,-18,8,9,9,9,10,-9,11,-9,12,-9,13,-9,14,9,15,9,16,12,17,-12,18,6,19,-6,20,-12,21,12,22,-6,23,6,24,12,25,-12,26,-12,27,12,28,6,29,-6,30,-6,31,6,32,6,33,6,34,3,35,3,36,-6,37,-6,38,-3,39,-3,40,6,41,6,42,-6,43,-6,44,3,45,3,46,-3,47,-3,48,8,49,-8,50,4,51,-4,52,4,53,-4,54,2,55,-2,56,4,57,4,58,2,59,2,60,2,61,2,62,1,63,1,
+        16,0,-6,2,6,4,6,6,-6,16,-3,18,-3,20,3,22,3,24,-4,26,4,28,-2,30,2,48,-2,50,-2,52,-1,54,-1,
+        16,8,-6,10,6,12,6,14,-6,32,-3,34,-3,36,3,38,3,40,-4,42,4,44,-2,46,2,56,-2,58,-2,60,-1,62,-1,
+        64,0,18,1,-18,2,-18,3,18,4,-18,5,18,6,18,7,-18,8,12,9,6,10,-12,11,-6,12,-12,13,-6,14,12,15,6,16,9,17,-9,18,9,19,-9,20,-9,21,9,22,-9,23,9,24,12,25,-12,26,-12,27,12,28,6,29,-6,30,-6,31,6,32,6,33,3,34,6,35,3,36,-6,37,-3,38,-6,39,-3,40,8,41,4,42,-8,43,-4,44,4,45,2,46,-4,47,-2,48,6,49,-6,50,6,51,-6,52,3,53,-3,54,3,55,-3,56,4,57,2,58,4,59,2,60,2,61,1,62,2,63,1,
+        64,0,-12,1,12,2,12,3,-12,4,12,5,-12,6,-12,7,12,8,-6,9,-6,10,6,11,6,12,6,13,6,14,-6,15,-6,16,-6,17,6,18,-6,19,6,20,6,21,-6,22,6,23,-6,24,-8,25,8,26,8,27,-8,28,-4,29,4,30,4,31,-4,32,-3,33,-3,34,-3,35,-3,36,3,37,3,38,3,39,3,40,-4,41,-4,42,4,43,4,44,-2,45,-2,46,2,47,2,48,-4,49,4,50,-4,51,4,52,-2,53,2,54,-2,55,2,56,-2,57,-2,58,-2,59,-2,60,-1,61,-1,62,-1,63,-1,
+        4,0,2,4,-2,24,1,28,1,
+        4,8,2,12,-2,40,1,44,1,
+        16,0,-6,1,6,4,6,5,-6,8,-4,9,-2,12,4,13,2,24,-3,25,3,28,-3,29,3,40,-2,41,-1,44,-2,45,-1,
+        16,0,4,1,-4,4,-4,5,4,8,2,9,2,12,-2,13,-2,24,2,25,-2,28,2,29,-2,40,1,41,1,44,1,45,1,
+        4,16,2,20,-2,48,1,52,1,
+        4,32,2,36,-2,56,1,60,1,
+        16,16,-6,17,6,20,6,21,-6,32,-4,33,-2,36,4,37,2,48,-3,49,3,52,-3,53,3,56,-2,57,-1,60,-2,61,-1,
+        16,16,4,17,-4,20,-4,21,4,32,2,33,2,36,-2,37,-2,48,2,49,-2,52,2,53,-2,56,1,57,1,60,1,61,1,
+        16,0,-6,2,6,4,6,6,-6,16,-4,18,-2,20,4,22,2,24,-3,26,3,28,-3,30,3,48,-2,50,-1,52,-2,54,-1,
+        16,8,-6,10,6,12,6,14,-6,32,-4,34,-2,36,4,38,2,40,-3,42,3,44,-3,46,3,56,-2,58,-1,60,-2,62,-1,
+        64,0,18,1,-18,2,-18,3,18,4,-18,5,18,6,18,7,-18,8,12,9,6,10,-12,11,-6,12,-12,13,-6,14,12,15,6,16,12,17,-12,18,6,19,-6,20,-12,21,12,22,-6,23,6,24,9,25,-9,26,-9,27,9,28,9,29,-9,30,-9,31,9,32,8,33,4,34,4,35,2,36,-8,37,-4,38,-4,39,-2,40,6,41,3,42,-6,43,-3,44,6,45,3,46,-6,47,-3,48,6,49,-6,50,3,51,-3,52,6,53,-6,54,3,55,-3,56,4,57,2,58,2,59,1,60,4,61,2,62,2,63,1,
+        64,0,-12,1,12,2,12,3,-12,4,12,5,-12,6,-12,7,12,8,-6,9,-6,10,6,11,6,12,6,13,6,14,-6,15,-6,16,-8,17,8,18,-4,19,4,20,8,21,-8,22,4,23,-4,24,-6,25,6,26,6,27,-6,28,-6,29,6,30,6,31,-6,32,-4,33,-4,34,-2,35,-2,36,4,37,4,38,2,39,2,40,-3,41,-3,42,3,43,3,44,-3,45,-3,46,3,47,3,48,-4,49,4,50,-2,51,2,52,-4,53,4,54,-2,55,2,56,-2,57,-2,58,-1,59,-1,60,-2,61,-2,62,-1,63,-1,
+        16,0,4,2,-4,4,-4,6,4,16,2,18,2,20,-2,22,-2,24,2,26,-2,28,2,30,-2,48,1,50,1,52,1,54,1,
+        16,8,4,10,-4,12,-4,14,4,32,2,34,2,36,-2,38,-2,40,2,42,-2,44,2,46,-2,56,1,58,1,60,1,62,1,
+        64,0,-12,1,12,2,12,3,-12,4,12,5,-12,6,-12,7,12,8,-8,9,-4,10,8,11,4,12,8,13,4,14,-8,15,-4,16,-6,17,6,18,-6,19,6,20,6,21,-6,22,6,23,-6,24,-6,25,6,26,6,27,-6,28,-6,29,6,30,6,31,-6,32,-4,33,-2,34,-4,35,-2,36,4,37,2,38,4,39,2,40,-4,41,-2,42,4,43,2,44,-4,45,-2,46,4,47,2,48,-3,49,3,50,-3,51,3,52,-3,53,3,54,-3,55,3,56,-2,57,-1,58,-2,59,-1,60,-2,61,-1,62,-2,63,-1,
+        64,0,8,1,-8,2,-8,3,8,4,-8,5,8,6,8,7,-8,8,4,9,4,10,-4,11,-4,12,-4,13,-4,14,4,15,4,16,4,17,-4,18,4,19,-4,20,-4,21,4,22,-4,23,4,24,4,25,-4,26,-4,27,4,28,4,29,-4,30,-4,31,4,32,2,33,2,34,2,35,2,36,-2,37,-2,38,-2,39,-2,40,2,41,2,42,-2,43,-2,44,2,45,2,46,-2,47,-2,48,2,49,-2,50,2,51,-2,52,2,53,-2,54,2,55,-2,56,1,57,1,58,1,59,1,60,1,61,1,62,1,63,1
+    };
+    vector<vector<int> > weight(64);
+    int index = 0;
+    for (int i = 0; i < 64; i++) {
+        int numElements = wt[index++];
+        for (int j = 0; j < numElements; j++) {
+            weight[i].push_back(wt[index++]);
+            weight[i].push_back(wt[index++]);
+        }
+    }
+    vector<double> rhs(64);
+    c.resize((xsize-1)*(ysize-1)*(zsize-1));
+    for (int i = 0; i < xsize-1; i++) {
+        for (int j = 0; j < ysize-1; j++) {
+            for (int k = 0; k < zsize-1; k++) {
+                // Compute the 64 coefficients for patch (i, j, k).
+
+                int nexti = i+1;
+                int nextj = j+1;
+                int nextk = k+1;
+                double deltax = x[nexti]-x[i];
+                double deltay = y[nextj]-y[j];
+                double deltaz = z[nextj]-z[j];
+                double e[] = {values[i+j*xsize+k*xysize], values[nexti+j*xsize+k*xysize], values[i+nextj*xsize+k*xysize], values[nexti+nextj*xsize+k*xysize], values[i+j*xsize+nextk*xysize], values[nexti+j*xsize+nextk*xysize], values[i+nextj*xsize+nextk*xysize], values[nexti+nextj*xsize+nextk*xysize]};
+                double e1[] = {d1[i+j*xsize+k*xysize], d1[nexti+j*xsize+k*xysize], d1[i+nextj*xsize+k*xysize], d1[nexti+nextj*xsize+k*xysize], d1[i+j*xsize+nextk*xysize], d1[nexti+j*xsize+nextk*xysize], d1[i+nextj*xsize+nextk*xysize], d1[nexti+nextj*xsize+nextk*xysize]};
+                double e2[] = {d2[i+j*xsize+k*xysize], d2[nexti+j*xsize+k*xysize], d2[i+nextj*xsize+k*xysize], d2[nexti+nextj*xsize+k*xysize], d2[i+j*xsize+nextk*xysize], d2[nexti+j*xsize+nextk*xysize], d2[i+nextj*xsize+nextk*xysize], d2[nexti+nextj*xsize+nextk*xysize]};
+                double e3[] = {d3[i+j*xsize+k*xysize], d3[nexti+j*xsize+k*xysize], d3[i+nextj*xsize+k*xysize], d3[nexti+nextj*xsize+k*xysize], d3[i+j*xsize+nextk*xysize], d3[nexti+j*xsize+nextk*xysize], d3[i+nextj*xsize+nextk*xysize], d3[nexti+nextj*xsize+nextk*xysize]};
+                double e12[] = {d12[i+j*xsize+k*xysize], d12[nexti+j*xsize+k*xysize], d12[i+nextj*xsize+k*xysize], d12[nexti+nextj*xsize+k*xysize], d12[i+j*xsize+nextk*xysize], d12[nexti+j*xsize+nextk*xysize], d12[i+nextj*xsize+nextk*xysize], d12[nexti+nextj*xsize+nextk*xysize]};
+                double e13[] = {d13[i+j*xsize+k*xysize], d13[nexti+j*xsize+k*xysize], d13[i+nextj*xsize+k*xysize], d13[nexti+nextj*xsize+k*xysize], d13[i+j*xsize+nextk*xysize], d13[nexti+j*xsize+nextk*xysize], d13[i+nextj*xsize+nextk*xysize], d13[nexti+nextj*xsize+nextk*xysize]};
+                double e23[] = {d23[i+j*xsize+k*xysize], d23[nexti+j*xsize+k*xysize], d23[i+nextj*xsize+k*xysize], d23[nexti+nextj*xsize+k*xysize], d23[i+j*xsize+nextk*xysize], d23[nexti+j*xsize+nextk*xysize], d23[i+nextj*xsize+nextk*xysize], d23[nexti+nextj*xsize+nextk*xysize]};
+                double e123[] = {d123[i+j*xsize+k*xysize], d123[nexti+j*xsize+k*xysize], d123[i+nextj*xsize+k*xysize], d123[nexti+nextj*xsize+k*xysize], d123[i+j*xsize+nextk*xysize], d123[nexti+j*xsize+nextk*xysize], d123[i+nextj*xsize+nextk*xysize], d123[nexti+nextj*xsize+nextk*xysize]};
+                for (int m = 0; m < 8; m++) {
+                    rhs[m] = e[m];
+                    rhs[m+8] = e1[m]*deltax;
+                    rhs[m+16] = e2[m]*deltay;
+                    rhs[m+24] = e3[m]*deltaz;
+                    rhs[m+32] = e12[m]*deltax*deltay;
+                    rhs[m+40] = e13[m]*deltax*deltaz;
+                    rhs[m+48] = e23[m]*deltay*deltaz;
+                    rhs[m+56] = e123[m]*deltax*deltay*deltaz;
+                }
+                vector<double>& coeff = c[i+j*(xsize-1)+k*(xsize-1)*(ysize-1)];
+                coeff.resize(64);
+                for (int m = 0; m < 64; m++) {
+                    double sum = 0.0;
+                    int numElements = weight[m].size();
+                    for (int n = 0; n < numElements; n += 2)
+                        sum += weight[m][n+1]*rhs[weight[m][n]];
+                    coeff[m] = sum;
+                }
+            }
+        }
+    }
+}
+
+double SplineFitter::evaluate3DSpline(const vector<double>& x, const vector<double>& y, const vector<double>& z, const vector<double>& values, const vector<vector<double> >& c, double u, double v, double w) {
+    int xsize = x.size();
+    int ysize = y.size();
+    int zsize = z.size();
+    if (u < x[0] || u > x[xsize-1] || v < y[0] || v > y[ysize-1] || w < z[0] || w > z[zsize-1])
+        throw OpenMMException("evaluate3DSpline: specified point is outside the range defined by the spline");
+
+    // Perform a binary search to identify the interval containing the point to evaluate.
+
+    int lowerx = 0;
+    int upperx = xsize-1;
+    while (upperx-lowerx > 1) {
+        int middle = (upperx+lowerx)/2;
+        if (x[middle] > u)
+            upperx = middle;
+        else
+            lowerx = middle;
+    }
+    int lowery = 0;
+    int uppery = ysize-1;
+    while (uppery-lowery > 1) {
+        int middle = (uppery+lowery)/2;
+        if (y[middle] > v)
+            uppery = middle;
+        else
+            lowery = middle;
+    }
+    int lowerz = 0;
+    int upperz = zsize-1;
+    while (upperz-lowerz > 1) {
+        int middle = (upperz+lowerz)/2;
+        if (z[middle] > w)
+            upperz = middle;
+        else
+            lowerz = middle;
+    }
+    double deltax = x[upperx]-x[lowerx];
+    double deltay = y[uppery]-y[lowery];
+    double deltaz = z[upperz]-z[lowerz];
+    double da = (u-x[lowerx])/deltax;
+    double db = (v-y[lowery])/deltay;
+    double dc = (w-z[lowerz])/deltaz;
+    const vector<double>& coeff = c[lowerx+(xsize-1)*lowery+(xsize-1)*(ysize-1)*lowerz];
+
+    // Evaluate the spline to determine the value and gradients.
+
+    double value[] = {0, 0, 0, 0};
+    for (int i = 3; i >= 0; i--) {
+        for (int j = 0; j < 4; j++) {
+            int base = 4*i + 16*j;
+            value[j] = db*value[j] + ((coeff[base+3]*da + coeff[base+2])*da + coeff[base+1])*da + coeff[base];
+        }
+    }
+    return value[0] + dc*(value[1] + dc*(value[2] + dc*value[3]));
+}
+
+void SplineFitter::evaluate3DSplineDerivatives(const vector<double>& x, const vector<double>& y, const vector<double>& z, const vector<double>& values, const vector<vector<double> >& c, double u, double v, double w, double& dx, double& dy, double& dz) {
+    int xsize = x.size();
+    int ysize = y.size();
+    int zsize = z.size();
+    if (u < x[0] || u > x[xsize-1] || v < y[0] || v > y[ysize-1] || w < z[0] || w > z[zsize-1])
+        throw OpenMMException("evaluate3DSpline: specified point is outside the range defined by the spline");
+
+    // Perform a binary search to identify the interval containing the point to evaluate.
+
+    int lowerx = 0;
+    int upperx = xsize-1;
+    while (upperx-lowerx > 1) {
+        int middle = (upperx+lowerx)/2;
+        if (x[middle] > u)
+            upperx = middle;
+        else
+            lowerx = middle;
+    }
+    int lowery = 0;
+    int uppery = ysize-1;
+    while (uppery-lowery > 1) {
+        int middle = (uppery+lowery)/2;
+        if (y[middle] > v)
+            uppery = middle;
+        else
+            lowery = middle;
+    }
+    int lowerz = 0;
+    int upperz = zsize-1;
+    while (upperz-lowerz > 1) {
+        int middle = (upperz+lowerz)/2;
+        if (z[middle] > w)
+            upperz = middle;
+        else
+            lowerz = middle;
+    }
+    double deltax = x[upperx]-x[lowerx];
+    double deltay = y[uppery]-y[lowery];
+    double deltaz = z[upperz]-z[lowerz];
+    double da = (u-x[lowerx])/deltax;
+    double db = (v-y[lowery])/deltay;
+    double dc = (w-z[lowerz])/deltaz;
+    const vector<double>& coeff = c[lowerx+(xsize-1)*lowery+(xsize-1)*(ysize-1)*lowerz];
+
+    // Evaluate the spline to determine the derivatives.
+
+    double derivx[] = {0, 0, 0, 0};
+    double derivy[] = {0, 0, 0, 0};
+    double derivz[] = {0, 0, 0, 0};
+    for (int i = 3; i >= 0; i--) {
+        for (int j = 0; j < 4; j++) {
+            int base = 4*i + 16*j;
+            derivx[j] = db*derivx[j] + (3.0*coeff[base+3]*da + 2.0*coeff[base+2])*da + coeff[base+1];
+            derivz[j] = db*derivz[j] + ((coeff[base+3]*da + coeff[base+2])*da + coeff[base+1])*da + coeff[base];
+            base = i + 16*j;
+            derivy[j] = da*derivy[j] + (3.0*coeff[base+12]*db + 2.0*coeff[base+8])*db + coeff[base+4];
+        }
+    }
+    dx = derivx[0] + dc*(derivx[1] + dc*(derivx[2] + dc*derivx[3]));
+    dy = derivy[0] + dc*(derivy[1] + dc*(derivy[2] + dc*derivy[3]));
+    dz = derivz[1] + dc*(2.0*derivz[2] + 3.0*dc*derivz[3]);
+    dx /= deltax;
+    dy /= deltay;
+    dz /= deltaz;
+}

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 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(vector<double>& values, double& min, double& max) const {
+    values = this->values;
+    min = this->min;
+    max = this->max;
+}
+
+void Continuous1DFunction::setFunctionParameters(const 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;
+}
+
+Continuous2DFunction::Continuous2DFunction(int xsize, int ysize, const vector<double>& values, double xmin, double xmax, double ymin, double ymax) {
+    if (xsize < 2 || ysize < 2)
+        throw OpenMMException("Continuous2DFunction: must have at least two points along each axis");
+    if (values.size() != xsize*ysize)
+        throw OpenMMException("Continuous2DFunction: incorrect number of values");
+    if (xmax <= xmin)
+        throw OpenMMException("Continuous2DFunction: xmax <= xmin for a tabulated function.");
+    if (ymax <= ymin)
+        throw OpenMMException("Continuous2DFunction: ymax <= ymin for a tabulated function.");
+    this->values = values;
+    this->xsize = xsize;
+    this->ysize = ysize;
+    this->xmin = xmin;
+    this->xmax = xmax;
+    this->ymin = ymin;
+    this->ymax = ymax;
+}
+
+void Continuous2DFunction::getFunctionParameters(int& xsize, int& ysize, vector<double>& values, double& xmin, double& xmax, double& ymin, double& ymax) const {
+    values = this->values;
+    xsize = this->xsize;
+    ysize = this->ysize;
+    xmin = this->xmin;
+    xmax = this->xmax;
+    ymin = this->ymin;
+    ymax = this->ymax;
+}
+
+void Continuous2DFunction::setFunctionParameters(int xsize, int ysize, const vector<double>& values, double xmin, double xmax, double ymin, double ymax) {
+    if (xsize < 2 || ysize < 2)
+        throw OpenMMException("Continuous2DFunction: must have at least two points along each axis");
+    if (values.size() != xsize*ysize)
+        throw OpenMMException("Continuous2DFunction: incorrect number of values");
+    if (xmax <= xmin)
+        throw OpenMMException("Continuous2DFunction: xmax <= xmin for a tabulated function.");
+    if (ymax <= ymin)
+        throw OpenMMException("Continuous2DFunction: ymax <= ymin for a tabulated function.");
+    this->values = values;
+    this->xsize = xsize;
+    this->ysize = ysize;
+    this->xmin = xmin;
+    this->xmax = xmax;
+    this->ymin = ymin;
+    this->ymax = ymax;
+}
+
+Continuous3DFunction::Continuous3DFunction(int xsize, int ysize, int zsize, const vector<double>& values, double xmin, double xmax, double ymin, double ymax, double zmin, double zmax) {
+    if (xsize < 2 || ysize < 2 || zsize < 2)
+        throw OpenMMException("Continuous3DFunction: must have at least two points along each axis");
+    if (values.size() != xsize*ysize*zsize)
+        throw OpenMMException("Continuous3DFunction: incorrect number of values");
+    if (xmax <= xmin)
+        throw OpenMMException("Continuous3DFunction: xmax <= xmin for a tabulated function.");
+    if (ymax <= ymin)
+        throw OpenMMException("Continuous3DFunction: ymax <= ymin for a tabulated function.");
+    if (zmax <= zmin)
+        throw OpenMMException("Continuous3DFunction: zmax <= zmin for a tabulated function.");
+    this->values = values;
+    this->xsize = xsize;
+    this->ysize = ysize;
+    this->zsize = zsize;
+    this->xmin = xmin;
+    this->xmax = xmax;
+    this->ymin = ymin;
+    this->ymax = ymax;
+    this->zmin = zmin;
+    this->zmax = zmax;
+}
+
+void Continuous3DFunction::getFunctionParameters(int& xsize, int& ysize, int& zsize, vector<double>& values, double& xmin, double& xmax, double& ymin, double& ymax, double& zmin, double& zmax) const {
+    values = this->values;
+    xsize = this->xsize;
+    ysize = this->ysize;
+    zsize = this->zsize;
+    xmin = this->xmin;
+    xmax = this->xmax;
+    ymin = this->ymin;
+    ymax = this->ymax;
+    zmin = this->zmin;
+    zmax = this->zmax;
+}
+
+void Continuous3DFunction::setFunctionParameters(int xsize, int ysize, int zsize, const vector<double>& values, double xmin, double xmax, double ymin, double ymax, double zmin, double zmax) {
+    if (xsize < 2 || ysize < 2 || zsize < 2)
+        throw OpenMMException("Continuous3DFunction: must have at least two points along each axis");
+    if (values.size() != xsize*ysize*zsize)
+        throw OpenMMException("Continuous3DFunction: incorrect number of values");
+    if (xmax <= xmin)
+        throw OpenMMException("Continuous3DFunction: xmax <= xmin for a tabulated function.");
+    if (ymax <= ymin)
+        throw OpenMMException("Continuous3DFunction: ymax <= ymin for a tabulated function.");
+    if (zmax <= zmin)
+        throw OpenMMException("Continuous3DFunction: zmax <= zmin for a tabulated function.");
+    this->values = values;
+    this->xsize = xsize;
+    this->ysize = ysize;
+    this->zsize = zsize;
+    this->xmin = xmin;
+    this->xmax = xmax;
+    this->ymin = ymin;
+    this->ymax = ymax;
+    this->zmin = zmin;
+    this->zmax = zmax;
+}
+
+Discrete1DFunction::Discrete1DFunction(const vector<double>& values) {
+    this->values = values;
+}
+
+void Discrete1DFunction::getFunctionParameters(vector<double>& values) const {
+    values = this->values;
+}
+
+void Discrete1DFunction::setFunctionParameters(const vector<double>& values) {
+    this->values = values;
+}
+
+Discrete2DFunction::Discrete2DFunction(int xsize, int ysize, const vector<double>& values) {
+    if (values.size() != xsize*ysize)
+        throw OpenMMException("Discrete2DFunction: incorrect number of values");
+    this->xsize = xsize;
+    this->ysize = ysize;
+    this->values = values;
+}
+
+void Discrete2DFunction::getFunctionParameters(int& xsize, int& ysize, vector<double>& values) const {
+    xsize = this->xsize;
+    ysize = this->ysize;
+    values = this->values;
+}
+
+void Discrete2DFunction::setFunctionParameters(int xsize, int ysize, const vector<double>& values) {
+    if (values.size() != xsize*ysize)
+        throw OpenMMException("Discrete2DFunction: incorrect number of values");
+    this->xsize = xsize;
+    this->ysize = ysize;
+    this->values = values;
+}
+
+Discrete3DFunction::Discrete3DFunction(int xsize, int ysize, int zsize, const vector<double>& values) {
+    if (values.size() != xsize*ysize*zsize)
+        throw OpenMMException("Discrete3DFunction: incorrect number of values");
+    this->xsize = xsize;
+    this->ysize = ysize;
+    this->zsize = zsize;
+    this->values = values;
+}
+
+void Discrete3DFunction::getFunctionParameters(int& xsize, int& ysize, int& zsize, vector<double>& values) const {
+    xsize = this->xsize;
+    ysize = this->ysize;
+    zsize = this->zsize;
+    values = this->values;
+}
+
+void Discrete3DFunction::setFunctionParameters(int xsize, int ysize, int zsize, const vector<double>& values) {
+    if (values.size() != xsize*ysize*zsize)
+        throw OpenMMException("Discrete3DFunction: incorrect number of values");
+    this->xsize = xsize;
+    this->ysize = ysize;
+    this->zsize = zsize;
+    this->values = values;
+}