Skip to content

GitLab

Commit dabc225e authored by peastman's avatar peastman
Browse files

Created new API for tabulated functions

parent 77a54244
Show whitespace changes
Inline Side-by-side
Showing with 458 additions and 154 deletions
openmmapi/include/OpenMM.h
View file @ dabc225e
......@@ -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 @ dabc225e
......@@ -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 addFunction() 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 {
......@@ -229,33 +230,54 @@ 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 addFunction(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& getFunction(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& getFunction(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& getFunctionName(int index);
/**
* Add a tabulated function that may appear in the energy expression.
*
* @deprecated This method exists only for backward compatibility. Use the version that takes
* a TabulatedFunction 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 the version that takes
* a TabulatedFunction 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 the version that takes
* a TabulatedFunction 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 +355,10 @@ 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 @ dabc225e
......@@ -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 addFunction() 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 {
......@@ -452,36 +453,57 @@ 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 addFunction(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& getFunction(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& getFunction(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& getFunctionName(int index);
/**
* Add a tabulated function that may appear in expressions.
*
* @deprecated This method exists only for backward compatibility. Use the version that takes
* a TabulatedFunction 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 the version that takes
* a TabulatedFunction 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 the version that takes
* a TabulatedFunction 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 +599,10 @@ 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 @ dabc225e
......@@ -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 addFunction() 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 {
......@@ -374,33 +375,54 @@ 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 addFunction(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& getFunction(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& getFunction(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& getFunctionName(int index);
/**
* Add a tabulated function that may appear in the energy expression.
*
* @deprecated This method exists only for backward compatibility. Use the version that takes
* a TabulatedFunction 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 the version that takes
* a TabulatedFunction 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 the version that takes
* a TabulatedFunction 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 +521,10 @@ 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 @ dabc225e
......@@ -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 addFunction() 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 {
......@@ -359,33 +360,54 @@ 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 addFunction(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& getFunction(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& getFunction(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& getFunctionName(int index);
/**
* Add a tabulated function that may appear in the energy expression.
*
* @deprecated This method exists only for backward compatibility. Use the version that takes
* a TabulatedFunction 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 the version that takes
* a TabulatedFunction 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 the version that takes
* a TabulatedFunction 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 +529,10 @@ 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 @ dabc225e
#ifndef OPENMM_TabulatedFunction_H_
#define OPENMM_TabulatedFunction_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "internal/windowsExport.h"
#include <vector>
namespace OpenMM {
/**
* A TabulatedFunction uses a set of tabulated values to define a mathematical function.
* It can be used by various custom forces.
*
* TabulatedFunction is an abstract class with concrete subclasses for more specific
* types of functions. There are subclasses for:
*
* <ul>
* <li>1, 2, and 3 dimensional functions. The dimensionality of a function means
* the number of input arguments it takes.</li>
* <li>Continuous and discrete functions. A continuous function is interpolated by
* fitting a natural cubic spline to the tabulated values. A discrete function is
* only defined for integer values of its arguments (that is, at the tabulated points),
* and does not try to interpolate between them. Discrete function can be evaluated
* more quickly than continuous ones.</li>
* </ul>
*/
class OPENMM_EXPORT TabulatedFunction {
public:
virtual ~TabulatedFunction() {
}
};
/**
* This is a TabulatedFunction that computes a continuous one dimensional function.
*/
class OPENMM_EXPORT Continuous1DFunction : public TabulatedFunction {
public:
/**
* Create a Continuous1DFunction f(x) based on a set of tabulated values.
*
* @param values the tabulated values of the function f(x) at uniformly spaced values of x between min
* and max. A natural cubic spline is used to interpolated between the tabulated values.
* The function is assumed to be zero for x &lt; min or x &gt; max.
* @param min the value of x corresponding to the first element of values
* @param max the value of x corresponding to the last element of values
*/
Continuous1DFunction(const std::vector<double>& values, double min, double max);
/**
* Get the parameters for the tabulated function.
*
* @param values the tabulated values of the function f(x) at uniformly spaced values of x between min
* and max. A natural cubic spline is used to interpolated between the tabulated values.
* The function is assumed to be zero for x &lt; min or x &gt; max.
* @param min the value of x corresponding to the first element of values
* @param max the value of x corresponding to the last element of values
*/
void getFunctionParameters(std::vector<double>& values, double& min, double& max) const;
/**
* Set the parameters for the tabulated function.
*
* @param values the tabulated values of the function f(x) at uniformly spaced values of x between min
* and max. A natural cubic spline is used to interpolated between the tabulated values.
* The function is assumed to be zero for x &lt; min or x &gt; max.
* @param min the value of x corresponding to the first element of values
* @param max the value of x corresponding to the last element of values
*/
void setFunctionParameters(const std::vector<double>& values, double min, double max);
private:
std::vector<double> values;
double min, max;
};
} // namespace OpenMM
#endif /*OPENMM_TabulatedFunction_H_*/
openmmapi/src/CustomCompoundBondForce.cpp
View file @ dabc225e
......@@ -120,33 +120,47 @@ void CustomCompoundBondForce::setBondParameters(int index, const vector<int>& pa
bonds[index].parameters = parameters;
}
int CustomCompoundBondForce::addFunction(const std::string& name, TabulatedFunction* function) {
functions.push_back(FunctionInfo(name, function));
return functions.size()-1;
}
const TabulatedFunction& CustomCompoundBondForce::getFunction(int index) const {
ASSERT_VALID_INDEX(index, functions);
return *functions[index].function;
}
TabulatedFunction& CustomCompoundBondForce::getFunction(int index) {
ASSERT_VALID_INDEX(index, functions);
return *functions[index].function;
}
const string& CustomCompoundBondForce::getFunctionName(int index) {
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/CustomGBForce.cpp
View file @ dabc225e
......@@ -173,33 +173,47 @@ void CustomGBForce::setExclusionParticles(int index, int particle1, int particle
exclusions[index].particle2 = particle2;
}
int CustomGBForce::addFunction(const std::string& name, TabulatedFunction* function) {
functions.push_back(FunctionInfo(name, function));
return functions.size()-1;
}
const TabulatedFunction& CustomGBForce::getFunction(int index) const {
ASSERT_VALID_INDEX(index, functions);
return *functions[index].function;
}
TabulatedFunction& CustomGBForce::getFunction(int index) {
ASSERT_VALID_INDEX(index, functions);
return *functions[index].function;
}
const string& CustomGBForce::getFunctionName(int index) {
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 @ dabc225e
......@@ -187,33 +187,47 @@ void CustomHbondForce::setExclusionParticles(int index, int donor, int acceptor)
exclusions[index].acceptor = acceptor;
}
int CustomHbondForce::addFunction(const std::string& name, TabulatedFunction* function) {
functions.push_back(FunctionInfo(name, function));
return functions.size()-1;
}
const TabulatedFunction& CustomHbondForce::getFunction(int index) const {
ASSERT_VALID_INDEX(index, functions);
return *functions[index].function;
}
TabulatedFunction& CustomHbondForce::getFunction(int index) {
ASSERT_VALID_INDEX(index, functions);
return *functions[index].function;
}
const string& CustomHbondForce::getFunctionName(int index) {
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 @ dabc225e
......@@ -169,34 +169,47 @@ void CustomNonbondedForce::setExclusionParticles(int index, int particle1, int p
exclusions[index].particle1 = particle1;
exclusions[index].particle2 = particle2;
}
int CustomNonbondedForce::addFunction(const std::string& name, TabulatedFunction* function) {
functions.push_back(FunctionInfo(name, function));
return functions.size()-1;
}
const TabulatedFunction& CustomNonbondedForce::getFunction(int index) const {
ASSERT_VALID_INDEX(index, functions);
return *functions[index].function;
}
TabulatedFunction& CustomNonbondedForce::getFunction(int index) {
ASSERT_VALID_INDEX(index, functions);
return *functions[index].function;
}
const string& CustomNonbondedForce::getFunctionName(int index) {
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/TabulatedFunction.cpp 0 → 100644
View file @ dabc225e
/* -------------------------------------------------------------------------- *
* 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 std::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(std::vector<double>& values, double& min, double& max) const {
values = this->values;
min = this->min;
max = this->max;
}
void Continuous1DFunction::setFunctionParameters(const std::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;
}
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment