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Commit 0fe7612b authored by peastman's avatar peastman
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Merge pull request #337 from peastman/functions 

Created new API for tabulated functions
parents 7a7055b3 ed31a458
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Showing with 2179 additions and 399 deletions
openmmapi/include/OpenMM.h
View file @ 0fe7612b
......@@ -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
View file @ 0fe7612b
......@@ -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
View file @ 0fe7612b
......@@ -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
View file @ 0fe7612b
......@@ -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
View file @ 0fe7612b
......@@ -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 0 → 100644
View file @ 0fe7612b
This diff is collapsed.
openmmapi/include/openmm/internal/SplineFitter.h
View file @ 0fe7612b
......@@ -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
View file @ 0fe7612b
......@@ -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
View file @ 0fe7612b
......@@ -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
View file @ 0fe7612b
......@@ -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
View file @ 0fe7612b
......@@ -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
View file @ 0fe7612b
......@@ -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
View file @ 0fe7612b
This diff is collapsed.
openmmapi/src/TabulatedFunction.cpp 0 → 100644
View file @ 0fe7612b
/* -------------------------------------------------------------------------- *
* 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;
}
platforms/cuda/include/CudaExpressionUtilities.h
View file @ 0fe7612b
......@@ -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) 2009-2012 Stanford University and the Authors. *
* Portions copyright (c) 2009-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -28,6 +28,7 @@
* -------------------------------------------------------------------------- */
#include "CudaContext.h"
#include "openmm/TabulatedFunction.h"
#include "lepton/CustomFunction.h"
#include "lepton/ExpressionTreeNode.h"
#include "lepton/ParsedExpression.h"
......@@ -45,65 +46,56 @@ namespace OpenMM {
class OPENMM_EXPORT_CUDA CudaExpressionUtilities {
public:
CudaExpressionUtilities(CudaContext& context) : context(context) {
}
CudaExpressionUtilities(CudaContext& context);
/**
* Generate the source code for calculating a set of expressions.
*
* @param expressions the expressions to generate code for (keys are the variables to store the output values in)
* @param variables defines the source code to generate for each variable that may appear in the expressions. Keys are
* variable names, and the values are the code to generate for them.
* @param functions defines the variable name for each tabulated function that may appear in the expressions
* @param functions the tabulated functions that may appear in the expressions
* @param functionNames defines the variable name for each tabulated function that may appear in the expressions
* @param prefix a prefix to put in front of temporary variables
* @param functionParams the variable name containing the parameters for each tabulated function
* @param tempType the type of value to use for temporary variables (defaults to "real")
*/
std::string createExpressions(const std::map<std::string, Lepton::ParsedExpression>& expressions, const std::map<std::string, std::string>& variables,
const std::vector<std::pair<std::string, std::string> >& functions, const std::string& prefix, const std::string& functionParams, const std::string& tempType="real");
const std::vector<const TabulatedFunction*>& functions, const std::vector<std::pair<std::string, std::string> >& functionNames,
const std::string& prefix, const std::string& tempType="real");
/**
* Generate the source code for calculating a set of expressions.
*
* @param expressions the expressions to generate code for (keys are the variables to store the output values in)
* @param variables defines the source code to generate for each variable or precomputed sub-expression that may appear in the expressions.
* Each entry is an ExpressionTreeNode, and the code to generate wherever an identical node appears.
* @param functions defines the variable name for each tabulated function that may appear in the expressions
* @param functions the tabulated functions that may appear in the expressions
* @param functionNames defines the variable name for each tabulated function that may appear in the expressions
* @param prefix a prefix to put in front of temporary variables
* @param functionParams the variable name containing the parameters for each tabulated function
* @param tempType the type of value to use for temporary variables (defaults to "real")
*/
std::string createExpressions(const std::map<std::string, Lepton::ParsedExpression>& expressions, const std::vector<std::pair<Lepton::ExpressionTreeNode, std::string> >& variables,
const std::vector<std::pair<std::string, std::string> >& functions, const std::string& prefix, const std::string& functionParams, const std::string& tempType="real");
const std::vector<const TabulatedFunction*>& functions, const std::vector<std::pair<std::string, std::string> >& functionNames,
const std::string& prefix, const std::string& tempType="real");
/**
* Calculate the spline coefficients for a tabulated function that appears in expressions.
*
* @param values the tabulated values of the function
* @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 the function for which to compute coefficients
* @param width on output, the number of floats used for each value
* @return the spline coefficients
*/
std::vector<float4> computeFunctionCoefficients(const std::vector<double>& values, double min, double max);
class FunctionPlaceholder;
private:
void processExpression(std::stringstream& out, const Lepton::ExpressionTreeNode& node,
std::vector<std::pair<Lepton::ExpressionTreeNode, std::string> >& temps,
const std::vector<std::pair<std::string, std::string> >& functions, const std::string& prefix, const std::string& functionParams,
const std::vector<Lepton::ParsedExpression>& allExpressions, const std::string& tempType);
std::string getTempName(const Lepton::ExpressionTreeNode& node, const std::vector<std::pair<Lepton::ExpressionTreeNode, std::string> >& temps);
void findRelatedTabulatedFunctions(const Lepton::ExpressionTreeNode& node, const Lepton::ExpressionTreeNode& searchNode,
const Lepton::ExpressionTreeNode*& valueNode, const Lepton::ExpressionTreeNode*& derivNode);
void findRelatedPowers(const Lepton::ExpressionTreeNode& node, const Lepton::ExpressionTreeNode& searchNode,
std::map<int, const Lepton::ExpressionTreeNode*>& powers);
CudaContext& context;
};
/**
* This class serves as a placeholder for custom functions in expressions.
std::vector<float> computeFunctionCoefficients(const TabulatedFunction& function, int& width);
/**
* Get a Lepton::CustomFunction that can be used to represent a TabulatedFunction when parsing expressions.
*
* @param function the function for which to get a placeholder
*/
class CudaExpressionUtilities::FunctionPlaceholder : public Lepton::CustomFunction {
public:
Lepton::CustomFunction* getFunctionPlaceholder(const TabulatedFunction& function);
private:
class FunctionPlaceholder : public Lepton::CustomFunction {
public:
FunctionPlaceholder(int numArgs) : numArgs(numArgs) {
}
int getNumArguments() const {
return 1;
return numArgs;
}
double evaluate(const double* arguments) const {
return 0.0;
......@@ -112,8 +104,23 @@ public:
return 0.0;
}
CustomFunction* clone() const {
return new FunctionPlaceholder();
return new FunctionPlaceholder(numArgs);
}
private:
int numArgs;
};
void processExpression(std::stringstream& out, const Lepton::ExpressionTreeNode& node,
std::vector<std::pair<Lepton::ExpressionTreeNode, std::string> >& temps,
const std::vector<const TabulatedFunction*>& functions, const std::vector<std::pair<std::string, std::string> >& functionNames,
const std::string& prefix, const std::vector<std::vector<double> >& functionParams, const std::vector<Lepton::ParsedExpression>& allExpressions, const std::string& tempType);
std::string getTempName(const Lepton::ExpressionTreeNode& node, const std::vector<std::pair<Lepton::ExpressionTreeNode, std::string> >& temps);
void findRelatedTabulatedFunctions(const Lepton::ExpressionTreeNode& node, const Lepton::ExpressionTreeNode& searchNode,
std::vector<const Lepton::ExpressionTreeNode*>& nodes);
void findRelatedPowers(const Lepton::ExpressionTreeNode& node, const Lepton::ExpressionTreeNode& searchNode,
std::map<int, const Lepton::ExpressionTreeNode*>& powers);
std::vector<std::vector<double> > computeFunctionParameters(const std::vector<const TabulatedFunction*>& functions);
CudaContext& context;
FunctionPlaceholder fp1, fp2, fp3;
};
} // namespace OpenMM
......
platforms/cuda/include/CudaKernels.h
View file @ 0fe7612b
......@@ -638,7 +638,7 @@ private:
class CudaCalcCustomNonbondedForceKernel : public CalcCustomNonbondedForceKernel {
public:
CudaCalcCustomNonbondedForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcCustomNonbondedForceKernel(name, platform),
cu(cu), params(NULL), globals(NULL), tabulatedFunctionParams(NULL), interactionGroupData(NULL), forceCopy(NULL), system(system), hasInitializedKernel(false) {
cu(cu), params(NULL), globals(NULL), interactionGroupData(NULL), forceCopy(NULL), system(system), hasInitializedKernel(false) {
}
~CudaCalcCustomNonbondedForceKernel();
/**
......@@ -669,7 +669,6 @@ private:
CudaContext& cu;
CudaParameterSet* params;
CudaArray* globals;
CudaArray* tabulatedFunctionParams;
CudaArray* interactionGroupData;
CUfunction interactionGroupKernel;
std::vector<void*> interactionGroupArgs;
......@@ -739,7 +738,7 @@ class CudaCalcCustomGBForceKernel : public CalcCustomGBForceKernel {
public:
CudaCalcCustomGBForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcCustomGBForceKernel(name, platform),
hasInitializedKernels(false), cu(cu), params(NULL), computedValues(NULL), energyDerivs(NULL), energyDerivChain(NULL), longEnergyDerivs(NULL), globals(NULL),
valueBuffers(NULL), tabulatedFunctionParams(NULL), system(system) {
valueBuffers(NULL), system(system) {
}
~CudaCalcCustomGBForceKernel();
/**
......@@ -776,7 +775,6 @@ private:
CudaArray* longEnergyDerivs;
CudaArray* globals;
CudaArray* valueBuffers;
CudaArray* tabulatedFunctionParams;
std::vector<std::string> globalParamNames;
std::vector<float> globalParamValues;
std::vector<CudaArray*> tabulatedFunctions;
......@@ -838,7 +836,7 @@ class CudaCalcCustomHbondForceKernel : public CalcCustomHbondForceKernel {
public:
CudaCalcCustomHbondForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcCustomHbondForceKernel(name, platform),
hasInitializedKernel(false), cu(cu), donorParams(NULL), acceptorParams(NULL), donors(NULL), acceptors(NULL),
globals(NULL), donorExclusions(NULL), acceptorExclusions(NULL), tabulatedFunctionParams(NULL), system(system) {
globals(NULL), donorExclusions(NULL), acceptorExclusions(NULL), system(system) {
}
~CudaCalcCustomHbondForceKernel();
/**
......@@ -875,7 +873,6 @@ private:
CudaArray* acceptors;
CudaArray* donorExclusions;
CudaArray* acceptorExclusions;
CudaArray* tabulatedFunctionParams;
std::vector<std::string> globalParamNames;
std::vector<float> globalParamValues;
std::vector<CudaArray*> tabulatedFunctions;
......@@ -890,7 +887,7 @@ private:
class CudaCalcCustomCompoundBondForceKernel : public CalcCustomCompoundBondForceKernel {
public:
CudaCalcCustomCompoundBondForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcCustomCompoundBondForceKernel(name, platform),
cu(cu), params(NULL), globals(NULL), tabulatedFunctionParams(NULL), system(system) {
cu(cu), params(NULL), globals(NULL), system(system) {
}
~CudaCalcCustomCompoundBondForceKernel();
/**
......@@ -922,7 +919,6 @@ private:
CudaContext& cu;
CudaParameterSet* params;
CudaArray* globals;
CudaArray* tabulatedFunctionParams;
std::vector<std::string> globalParamNames;
std::vector<float> globalParamValues;
std::vector<CudaArray*> tabulatedFunctions;
......
platforms/cuda/src/CudaKernels.cpp
View file @ 0fe7612b
This diff is collapsed.
platforms/cuda/tests/TestCudaCustomCompoundBondForce.cpp
View file @ 0fe7612b
......@@ -199,6 +199,103 @@ void testParallelComputation() {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
}
void testContinuous2DFunction() {
const int xsize = 10;
const int ysize = 11;
const double xmin = 0.4;
const double xmax = 1.1;
const double ymin = 0.0;
const double ymax = 0.9;
System system;
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomCompoundBondForce* forceField = new CustomCompoundBondForce(1, "fn(x1,y1)+1");
vector<int> particles(1, 0);
forceField->addBond(particles, vector<double>());
vector<double> table(xsize*ysize);
for (int i = 0; i < xsize; i++) {
for (int j = 0; j < ysize; j++) {
double x = xmin + i*(xmax-xmin)/xsize;
double y = ymin + j*(ymax-ymin)/ysize;
table[i+xsize*j] = sin(0.25*x)*cos(0.33*y);
}
}
forceField->addTabulatedFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(1);
for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
positions[0] = Vec3(x, y, 1.5);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double energy = 1;
Vec3 force(0, 0, 0);
if (x >= xmin && x <= xmax && y >= ymin && y <= ymax) {
energy = sin(0.25*x)*cos(0.33*y)+1;
force[0] = -0.25*cos(0.25*x)*cos(0.33*y);
force[1] = 0.3*sin(0.25*x)*sin(0.33*y);
}
ASSERT_EQUAL_VEC(force, forces[0], 0.1);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.05);
}
}
}
void testContinuous3DFunction() {
const int xsize = 10;
const int ysize = 11;
const int zsize = 12;
const double xmin = 0.4;
const double xmax = 1.1;
const double ymin = 0.0;
const double ymax = 0.9;
const double zmin = 0.2;
const double zmax = 1.3;
System system;
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomCompoundBondForce* forceField = new CustomCompoundBondForce(1, "fn(x1,y1,z1)+1");
vector<int> particles(1, 0);
forceField->addBond(particles, vector<double>());
vector<double> table(xsize*ysize*zsize);
for (int i = 0; i < xsize; i++) {
for (int j = 0; j < ysize; j++) {
for (int k = 0; k < zsize; k++) {
double x = xmin + i*(xmax-xmin)/xsize;
double y = ymin + j*(ymax-ymin)/ysize;
double z = zmin + k*(zmax-zmin)/zsize;
table[i+xsize*j+xsize*ysize*k] = sin(0.25*x)*cos(0.33*y)*(1+z);
}
}
}
forceField->addTabulatedFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(1);
for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
for (double z = zmin-0.15; z < zmax+0.2; z += 0.1) {
positions[0] = Vec3(x, y, z);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double energy = 1;
Vec3 force(0, 0, 0);
if (x >= xmin && x <= xmax && y >= ymin && y <= ymax && z >= zmin && z <= zmax) {
energy = sin(0.25*x)*cos(0.33*y)*(1.0+z)+1;
force[0] = -0.25*cos(0.25*x)*cos(0.33*y)*(1.0+z);
force[1] = 0.3*sin(0.25*x)*sin(0.33*y)*(1.0+z);
force[2] = -sin(0.25*x)*cos(0.33*y);
}
ASSERT_EQUAL_VEC(force, forces[0], 0.1);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.05);
}
}
}
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
......@@ -206,6 +303,8 @@ int main(int argc, char* argv[]) {
testBond();
testPositionDependence();
testParallelComputation();
testContinuous2DFunction();
testContinuous3DFunction();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
platforms/cuda/tests/TestCudaCustomGBForce.cpp
View file @ 0fe7612b
......@@ -277,7 +277,7 @@ void testTabulatedFunction() {
vector<double> table;
for (int i = 0; i < 21; i++)
table.push_back(std::sin(0.25*i));
force->addFunction("fn", table, 1.0, 6.0);
force->addTabulatedFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
system.addForce(force);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
......
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