Merge pull request #1294 from pandegroup/rmcgibbo-patch-1

Update CustomHbondForce.h

olla/include/openmm/Kernel.h

@@ -62,7 +62,7 @@ public:
     /**
      * Create a Kernel that wraps a KernelImpl.
      *
-     * @param name the name of the kernel to create
+     * @param KernelImpl the KernelImpl to wrap
      */
     Kernel(KernelImpl* impl);
     ~Kernel();

openmmapi/include/openmm/CustomHbondForce.h

@@ -369,8 +369,8 @@ public:
      * Get the donor and acceptor in a pair whose interaction should be excluded.
      *
      * @param index           the index of the exclusion for which to get donor and acceptor indices
-     * @param[out] particle1  the index of the donor
-     * @param[out] particle2  the index of the acceptor
+     * @param[out] donor      the index of the donor
+     * @param[out] acceptor   the index of the acceptor
      */
     void getExclusionParticles(int index, int& donor, int& acceptor) const;
     /**

openmmapi/include/openmm/TabulatedFunction.h

@@ -80,11 +80,11 @@ public:
     /**
      * 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
+     * @param[out] 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 < 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[out] min            the value of x corresponding to the first element of values
+     * @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;
     /**
@@ -129,16 +129,16 @@ public:
     /**
      * 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
+     * @param[out] 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
+     * @param[out] xsize      the number of table elements along the x direction
+     * @param[out] ysize      the number of table elements along the y direction
+     * @param[out] xmin       the value of x corresponding to the first element of values
+     * @param[out] xmax       the value of x corresponding to the last element of values
+     * @param[out] ymin       the value of y corresponding to the first element of values
+     * @param[out] 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;
     /**
@@ -194,21 +194,21 @@ public:
     /**
      * 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
+     * @param[out] 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
+     * @param[out] xsize      the number of table elements along the x direction
+     * @param[out] ysize      the number of table elements along the y direction
+     * @param[out] zsize      the number of table elements along the z direction
+     * @param[out] xmin       the value of x corresponding to the first element of values
+     * @param[out] xmax       the value of x corresponding to the last element of values
+     * @param[out] ymin       the value of y corresponding to the first element of values
+     * @param[out] ymax       the value of y corresponding to the last element of values
+     * @param[out] zmin       the value of z corresponding to the first element of values
+     * @param[out] 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;
     /**
@@ -222,7 +222,7 @@ public:
      *                   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 zsize      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
@@ -257,7 +257,7 @@ public:
     /**
      * Get the parameters for the tabulated function.
      *
-     * @param values         the tabulated values of the function f(x)
+     * @param[out] values    the tabulated values of the function f(x)
      */
     void getFunctionParameters(std::vector<double>& values) const;
     /**
@@ -293,9 +293,9 @@ public:
     /**
      * 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
+     * @param[out] xsize     the number of table elements along the x direction
+     * @param[out] ysize     the number of table elements along the y direction
+     * @param[out] 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;
@@ -337,10 +337,10 @@ public:
     /**
      * 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
+     * @param[out] xsize     the number of table elements along the x direction
+     * @param[out] ysize     the number of table elements along the y direction
+     * @param[out] zsize     the number of table elements along the z direction
+     * @param[out] 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;