Periodic 2D and 3D tabulated functions included in API

openmmapi/include/openmm/TabulatedFunction.h

@@ -63,6 +63,19 @@ public:
      * @deprecated This will be removed in a future release.
      */
     virtual TabulatedFunction* Copy() const = 0;
+    /**
+     * Get the periodicity status of the tabulated function.
+     *
+     */
+    bool getPeriodic() const;
+    /**
+     * Set the periodicity status for the tabulated function.
+     *
+     * @param periodic       whether the function is periodic with period L = max - min
+     */
+    void setPeriodic(bool periodic);
+protected:
+    bool periodic;
 };
 
 /**
@@ -78,7 +91,7 @@ public:
      *                       The function is assumed to be zero for x < min or x > 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
-     * @param periodic       whether the function is periodic with period L = max - min
+     * @param periodic       whether the interpolated function is periodic
      */
     Continuous1DFunction(const std::vector<double>& values, double min, double max, bool periodic=false);
     /**
@@ -91,11 +104,6 @@ public:
      * @param[out] max            the value of x corresponding to the last element of values
      */
     void getFunctionParameters(std::vector<double>& values, double& min, double& max) const;
-    /**
-     * Get the periodicity status of the tabulated function.
-     *
-     */
-    bool getPeriodic() const;
     /**
      * Set the parameters for the tabulated function.
      *
@@ -106,12 +114,6 @@ public:
      * @param max            the value of x corresponding to the last element of values
      */
     void setFunctionParameters(const std::vector<double>& values, double min, double max);
-    /**
-     * Set the periodicity status for the tabulated function.
-     *
-     * @param periodic       whether the function is periodic with period L = max - min
-     */
-    void setPeriodic(bool periodic);
     /**
      * Create a deep copy of the tabulated function.
      *
@@ -121,7 +123,6 @@ public:
 private:
     std::vector<double> values;
     double min, max;
-    bool periodic;
 };
 
 /**
@@ -142,8 +143,9 @@ public:
      * @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 periodic       whether the interpolated function is periodic
      */
-    Continuous2DFunction(int xsize, int ysize, const std::vector<double>& values, double xmin, double xmax, double ymin, double ymax);
+    Continuous2DFunction(int xsize, int ysize, const std::vector<double>& values, double xmin, double xmax, double ymin, double ymax, bool periodic=false);
     /**
      * Get the parameters for the tabulated function.
      *
@@ -209,8 +211,9 @@ public:
      * @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
+     * @param periodic       whether the interpolated function is periodic
      */
-    Continuous3DFunction(int xsize, int ysize, int zsize, const std::vector<double>& values, double xmin, double xmax, double ymin, double ymax, double zmin, double zmax);
+    Continuous3DFunction(int xsize, int ysize, int zsize, const std::vector<double>& values, double xmin, double xmax, double ymin, double ymax, double zmin, double zmax, bool periodic=false);
     /**
      * Get the parameters for the tabulated function.
      *

openmmapi/src/TabulatedFunction.cpp

@@ -35,6 +35,14 @@
 using namespace OpenMM;
 using namespace std;
 
+bool TabulatedFunction::getPeriodic() const {
+    return periodic;
+}
+
+void TabulatedFunction::setPeriodic(bool periodic) {
+    this->periodic = periodic;
+}
+
 Continuous1DFunction::Continuous1DFunction(const vector<double>& values, double min, double max, bool periodic) {
     this->periodic = periodic;
     setFunctionParameters(values, min, max);
@@ -46,10 +54,6 @@ void Continuous1DFunction::getFunctionParameters(vector<double>& values, double&
     max = this->max;
 }
 
-bool Continuous1DFunction::getPeriodic() const {
-    return periodic;
-}
-
 void Continuous1DFunction::setFunctionParameters(const vector<double>& values, double min, double max) {
     if (max <= min)
         throw OpenMMException("Continuous1DFunction: max <= min for a tabulated function.");
@@ -67,10 +71,6 @@ void Continuous1DFunction::setFunctionParameters(const vector<double>& values, d
     this->max = max;
 }
 
-void Continuous1DFunction::setPeriodic(bool periodic) {
-    this->periodic = periodic;
-}
-
 Continuous1DFunction* Continuous1DFunction::Copy() const {
     vector<double> new_vec(values.size());
     for (size_t i = 0; i < values.size(); i++)
@@ -78,22 +78,9 @@ Continuous1DFunction* Continuous1DFunction::Copy() const {
     return new Continuous1DFunction(new_vec, min, 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;
+Continuous2DFunction::Continuous2DFunction(int xsize, int ysize, const vector<double>& values, double xmin, double xmax, double ymin, double ymax, bool periodic) {
+    this->periodic = periodic;
+    setFunctionParameters(xsize, ysize, values, xmin, xmax, ymin, ymax);
 }
 
 void Continuous2DFunction::getFunctionParameters(int& xsize, int& ysize, vector<double>& values, double& xmin, double& xmax, double& ymin, double& ymax) const {
@@ -107,7 +94,13 @@ void Continuous2DFunction::getFunctionParameters(int& xsize, int& ysize, vector<
 }
 
 void Continuous2DFunction::setFunctionParameters(int xsize, int ysize, const vector<double>& values, double xmin, double xmax, double ymin, double ymax) {
-    if (xsize < 2 || ysize < 2)
+    if (periodic) {
+        if (xsize < 3 || ysize < 3)
+           throw OpenMMException("Continuous2DFunction: must have at least three points along each axis if periodic");
+
+        // Note: value-matching at boundary is eventually checked at 2D-spline creation time.
+    }
+    else 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");
@@ -131,27 +124,9 @@ Continuous2DFunction* Continuous2DFunction::Copy() const {
     return new Continuous2DFunction(xsize, ysize, new_vec, xmin, xmax, ymin, 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;
+Continuous3DFunction::Continuous3DFunction(int xsize, int ysize, int zsize, const vector<double>& values, double xmin, double xmax, double ymin, double ymax, double zmin, double zmax, bool periodic) {
+    this->periodic = periodic;
+    setFunctionParameters(xsize, ysize, zsize, values, xmin, xmax, ymin, ymax, zmin, 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 {
@@ -168,7 +143,13 @@ void Continuous3DFunction::getFunctionParameters(int& xsize, int& ysize, int& zs
 }
 
 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)
+    if (periodic) {
+       if (xsize < 3 || ysize < 3 || zsize < 3)
+           throw OpenMMException("Continuous3DFunction: must have at least three points along each axis if periodic");
+
+       // Note: value-matching at boundary is eventually checked at 3D-spline creation time.
+    }
+    else 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");