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Commit 90fea164 authored by Robert T. McGibbon's avatar Robert T. McGibbon
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Other header updates to bring docs into consistency with function signatures

parent 322bd639
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olla/include/openmm/Kernel.h
View file @ 90fea164
......@@ -40,16 +40,16 @@ namespace OpenMM {
/**
* A Kernel encapsulates a particular implementation of a calculation that can be performed on the data
* in a Context. Kernel objects are created by Platforms:
*
*
* <pre>
* Kernel kernel = platform.createKernel(kernelName);
* </pre>
*
*
* The Kernel class itself does not specify any details of what calculation is to be performed or the API
* for calling it. Instead, subclasses of KernelImpl will define APIs which are appropriate to particular
* calculations. To execute a Kernel, you therefore request its implementation object and cast it to the
* correct type:
*
*
* <pre>
* dynamic_cast<AddStreamsImpl&>(kernel.getImpl()).execute(stream1, stream2);
* </pre>
......@@ -61,8 +61,8 @@ public:
Kernel(const Kernel& copy);
/**
* 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/TabulatedFunction.h
View file @ 90fea164
......@@ -40,10 +40,10 @@ 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>
......@@ -69,7 +69,7 @@ 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.
......@@ -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
* 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
* @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 &lt; min or x &gt; max.
* @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;
/**
......@@ -113,7 +113,7 @@ 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
......@@ -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
* 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] 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[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;
/**
......@@ -173,7 +173,7 @@ 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
......@@ -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
* 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] 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[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
......@@ -250,14 +250,14 @@ 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)
* @param[out] values the tabulated values of the function f(x)
*/
void getFunctionParameters(std::vector<double>& values) const;
/**
......@@ -283,7 +283,7 @@ 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
......@@ -293,10 +293,10 @@ 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 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.
* @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;
/**
......@@ -326,7 +326,7 @@ 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
......@@ -337,11 +337,11 @@ 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
* values[i+xsize*j+xsize*ysize*k] = f(i,j,k). This must be of length xsize*ysize*zsize.
* @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;
/**
......
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