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Commit cf8a03e8 authored by peastman's avatar peastman
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openmmapi/include/OpenMM.h
View file @ cf8a03e8
......@@ -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/AndersenThermostat.h
View file @ cf8a03e8
......@@ -74,6 +74,15 @@ public:
double getDefaultTemperature() const {
return defaultTemp;
}
/**
* Set the default temperature of the heat bath. This will affect any new Contexts you create,
* but not ones that already exist.
*
* @param temperature the default temperature of the heat bath (in Kelvin)
*/
void setDefaultTemperature(double temperature) {
defaultTemp = temperature;
}
/**
* Get the default collision frequency (in 1/ps).
*
......@@ -82,6 +91,15 @@ public:
double getDefaultCollisionFrequency() const {
return defaultFreq;
}
/**
* Set the default collision frequency. This will affect any new Contexts you create,
* but not ones that already exist.
*
* @param frequency the default collision frequency (in 1/ps)
*/
void setDefaultCollisionFrequency(double frequency) {
defaultFreq = frequency;
}
/**
* Get the random number seed. See setRandomNumberSeed() for details.
*/
......
openmmapi/include/openmm/CustomCompoundBondForce.h
View file @ cf8a03e8
......@@ -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/CustomExternalForce.h
View file @ cf8a03e8
......@@ -61,7 +61,7 @@ namespace OpenMM {
* This force depends on four parameters: the spring constant k and equilibrium coordinates x0, y0, and z0. The following code defines these parameters:
*
* <tt><pre>
* force->addGlobalParameter("k");
* force->addGlobalParameter("k", 100.0);
* force->addPerParticleParameter("x0");
* force->addPerParticleParameter("y0");
* force->addPerParticleParameter("z0");
......
openmmapi/include/openmm/CustomGBForce.h
View file @ cf8a03e8
......@@ -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 @ cf8a03e8
......@@ -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 @ cf8a03e8
......@@ -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/MonteCarloAnisotropicBarostat.h
View file @ cf8a03e8
......@@ -100,6 +100,15 @@ public:
const Vec3& getDefaultPressure() const {
return defaultPressure;
}
/**
* Set the default pressure acting on the system. This will affect any new Contexts you create,
* but not ones that already exist.
*
* @param pressure the default pressure acting on the system, measured in bar.
*/
void setDefaultPressure(const Vec3& pressure) {
defaultPressure = pressure;
}
/**
* Get whether to allow the X dimension of the periodic box to change size.
*/
......
openmmapi/include/openmm/MonteCarloBarostat.h
View file @ cf8a03e8
......@@ -74,6 +74,15 @@ public:
double getDefaultPressure() const {
return defaultPressure;
}
/**
* Set the default pressure acting on the system. This will affect any new Contexts you create,
* but not ones that already exist.
*
* @param pressure the default pressure acting on the system, measured in bar.
*/
void setDefaultPressure(double pressure) {
defaultPressure = pressure;
}
/**
* Get the frequency (in time steps) at which Monte Carlo pressure changes should be attempted. If this is set to
* 0, the barostat is disabled.
......
openmmapi/include/openmm/NonbondedForce.h
View file @ cf8a03e8
......@@ -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: *
* *
......@@ -182,15 +182,41 @@ public:
* which is acceptable. This value is used to select the reciprocal space cutoff and separation
* parameter so that the average error level will be less than the tolerance. There is not a
* rigorous guarantee that all forces on all atoms will be less than the tolerance, however.
*
* For PME calculations, if setPMEParameters() is used to set alpha to something other than 0,
* this value is ignored.
*/
double getEwaldErrorTolerance() const;
/**
* Get the error tolerance for Ewald summation. This corresponds to the fractional error in the forces
* Set the error tolerance for Ewald summation. This corresponds to the fractional error in the forces
* which is acceptable. This value is used to select the reciprocal space cutoff and separation
* parameter so that the average error level will be less than the tolerance. There is not a
* rigorous guarantee that all forces on all atoms will be less than the tolerance, however.
*
* For PME calculations, if setPMEParameters() is used to set alpha to something other than 0,
* this value is ignored.
*/
void setEwaldErrorTolerance(double tol);
/**
* Get the parameters to use for PME calculations. If alpha is 0 (the default), these parameters are
* ignored and instead their values are chosen based on the Ewald error tolerance.
*
* @param alpha the separation parameter
* @param nx the number of grid points along the X axis
* @param ny the number of grid points along the Y axis
* @param nz the number of grid points along the Z axis
*/
void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
/**
* Set the parameters to use for PME calculations. If alpha is 0 (the default), these parameters are
* ignored and instead their values are chosen based on the Ewald error tolerance.
*
* @param alpha the separation parameter
* @param nx the number of grid points along the X axis
* @param ny the number of grid points along the Y axis
* @param nz the number of grid points along the Z axis
*/
void setPMEParameters(double alpha, int nx, int ny, int nz);
/**
* Add the nonbonded force parameters for a particle. This should be called once for each particle
* in the System. When it is called for the i'th time, it specifies the parameters for the i'th particle.
......@@ -332,9 +358,9 @@ private:
class ParticleInfo;
class ExceptionInfo;
NonbondedMethod nonbondedMethod;
double cutoffDistance, switchingDistance, rfDielectric, ewaldErrorTol;
double cutoffDistance, switchingDistance, rfDielectric, ewaldErrorTol, alpha;
bool useSwitchingFunction, useDispersionCorrection;
int recipForceGroup;
int recipForceGroup, nx, ny, nz;
void addExclusionsToSet(const std::vector<std::set<int> >& bonded12, std::set<int>& exclusions, int baseParticle, int fromParticle, int currentLevel) const;
std::vector<ParticleInfo> particles;
std::vector<ExceptionInfo> exceptions;
......
openmmapi/include/openmm/TabulatedFunction.h 0 → 100644
View file @ cf8a03e8
#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 interpolate between the tabulated values.
* The function is assumed to be zero for x &lt; min or x &gt; max.
* @param min the value of x corresponding to the first element of values
* @param max the value of x corresponding to the last element of values
*/
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 interpolate between the tabulated values.
* The function is assumed to be zero for x &lt; min or x &gt; max.
* @param min the value of x corresponding to the first element of values
* @param max the value of x corresponding to the last element of values
*/
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 interpolate between the tabulated values.
* The function is assumed to be zero for x &lt; min or x &gt; max.
* @param min the value of x corresponding to the first element of values
* @param max the value of x corresponding to the last element of values
*/
void setFunctionParameters(const std::vector<double>& values, double min, double max);
private:
std::vector<double> values;
double min, max;
};
/**
* This is a TabulatedFunction that computes a continuous two dimensional function.
*/
class OPENMM_EXPORT Continuous2DFunction : public TabulatedFunction {
public:
/**
* Create a Continuous2DFunction f(x,y) based on a set of tabulated values.
*
* @param values the tabulated values of the function f(x,y) at xsize uniformly spaced values of x between xmin
* and xmax, and ysize values of y between ymin and ymax. A natural cubic spline is used to interpolate between the tabulated values.
* The function is assumed to be zero when x or y is outside its specified range. The values should be ordered so that
* values[i+xsize*j] = f(x_i,y_j), where x_i is the i'th uniformly spaced value of x. This must be of length xsize*ysize.
* @param xsize the number of table elements along the x direction
* @param ysize the number of table elements along the y direction
* @param xmin the value of x corresponding to the first element of values
* @param xmax the value of x corresponding to the last element of values
* @param ymin the value of y corresponding to the first element of values
* @param ymax the value of y corresponding to the last element of values
*/
Continuous2DFunction(int xsize, int ysize, const std::vector<double>& values, double xmin, double xmax, double ymin, double ymax);
/**
* Get the parameters for the tabulated function.
*
* @param values the tabulated values of the function f(x,y) at xsize uniformly spaced values of x between xmin
* and xmax, and ysize values of y between ymin and ymax. A natural cubic spline is used to interpolate between the tabulated values.
* The function is assumed to be zero when x or y is outside its specified range. The values should be ordered so that
* values[i+xsize*j] = f(x_i,y_j), where x_i is the i'th uniformly spaced value of x. This must be of length xsize*ysize.
* @param xsize the number of table elements along the x direction
* @param ysize the number of table elements along the y direction
* @param xmin the value of x corresponding to the first element of values
* @param xmax the value of x corresponding to the last element of values
* @param ymin the value of y corresponding to the first element of values
* @param ymax the value of y corresponding to the last element of values
*/
void getFunctionParameters(int& xsize, int& ysize, std::vector<double>& values, double& xmin, double& xmax, double& ymin, double& ymax) const;
/**
* Set the parameters for the tabulated function.
*
* @param values the tabulated values of the function f(x,y) at xsize uniformly spaced values of x between xmin
* and xmax, and ysize values of y between ymin and ymax. A natural cubic spline is used to interpolate between the tabulated values.
* The function is assumed to be zero when x or y is outside its specified range. The values should be ordered so that
* values[i+xsize*j] = f(x_i,y_j), where x_i is the i'th uniformly spaced value of x. This must be of length xsize*ysize.
* @param xsize the number of table elements along the x direction
* @param ysize the number of table elements along the y direction
* @param xmin the value of x corresponding to the first element of values
* @param xmax the value of x corresponding to the last element of values
* @param ymin the value of y corresponding to the first element of values
* @param ymax the value of y corresponding to the last element of values
*/
void setFunctionParameters(int xsize, int ysize, const std::vector<double>& values, double xmin, double xmax, double ymin, double ymax);
private:
std::vector<double> values;
int xsize, ysize;
double xmin, xmax, ymin, ymax;
};
/**
* This is a TabulatedFunction that computes a continuous three dimensional function.
*/
class OPENMM_EXPORT Continuous3DFunction : public TabulatedFunction {
public:
/**
* Create a Continuous3DFunction f(x,y,z) based on a set of tabulated values.
*
* @param values the tabulated values of the function f(x,y,z) at xsize uniformly spaced values of x between xmin
* and xmax, ysize values of y between ymin and ymax, and zsize values of z between zmin and zmax.
* A natural cubic spline is used to interpolate between the tabulated values. The function is
* assumed to be zero when x, y, or z is outside its specified range. The values should be ordered so
* that values[i+xsize*j+xsize*ysize*k] = f(x_i,y_j,z_k), where x_i is the i'th uniformly spaced value of x.
* This must be of length xsize*ysize*zsize.
* @param xsize the number of table elements along the x direction
* @param ysize the number of table elements along the y direction
* @param ysize the number of table elements along the z direction
* @param xmin the value of x corresponding to the first element of values
* @param xmax the value of x corresponding to the last element of values
* @param ymin the value of y corresponding to the first element of values
* @param ymax the value of y corresponding to the last element of values
* @param zmin the value of z corresponding to the first element of values
* @param zmax the value of z corresponding to the last element of values
*/
Continuous3DFunction(int xsize, int ysize, int zsize, const std::vector<double>& values, double xmin, double xmax, double ymin, double ymax, double zmin, double zmax);
/**
* Get the parameters for the tabulated function.
*
* @param values the tabulated values of the function f(x,y,z) at xsize uniformly spaced values of x between xmin
* and xmax, ysize values of y between ymin and ymax, and zsize values of z between zmin and zmax.
* A natural cubic spline is used to interpolate between the tabulated values. The function is
* assumed to be zero when x, y, or z is outside its specified range. The values should be ordered so
* that values[i+xsize*j+xsize*ysize*k] = f(x_i,y_j,z_k), where x_i is the i'th uniformly spaced value of x.
* This must be of length xsize*ysize*zsize.
* @param xsize the number of table elements along the x direction
* @param ysize the number of table elements along the y direction
* @param ysize the number of table elements along the z direction
* @param xmin the value of x corresponding to the first element of values
* @param xmax the value of x corresponding to the last element of values
* @param ymin the value of y corresponding to the first element of values
* @param ymax the value of y corresponding to the last element of values
* @param zmin the value of z corresponding to the first element of values
* @param zmax the value of z corresponding to the last element of values
*/
void getFunctionParameters(int& xsize, int& ysize, int& zsize, std::vector<double>& values, double& xmin, double& xmax, double& ymin, double& ymax, double& zmin, double& zmax) const;
/**
* Set the parameters for the tabulated function.
*
* @param values the tabulated values of the function f(x,y,z) at xsize uniformly spaced values of x between xmin
* and xmax, ysize values of y between ymin and ymax, and zsize values of z between zmin and zmax.
* A natural cubic spline is used to interpolate between the tabulated values. The function is
* assumed to be zero when x, y, or z is outside its specified range. The values should be ordered so
* that values[i+xsize*j+xsize*ysize*k] = f(x_i,y_j,z_k), where x_i is the i'th uniformly spaced value of x.
* This must be of length xsize*ysize*zsize.
* @param xsize the number of table elements along the x direction
* @param ysize the number of table elements along the y direction
* @param ysize the number of table elements along the z direction
* @param xmin the value of x corresponding to the first element of values
* @param xmax the value of x corresponding to the last element of values
* @param ymin the value of y corresponding to the first element of values
* @param ymax the value of y corresponding to the last element of values
* @param zmin the value of z corresponding to the first element of values
* @param zmax the value of z corresponding to the last element of values
*/
void setFunctionParameters(int xsize, int ysize, int zsize, const std::vector<double>& values, double xmin, double xmax, double ymin, double ymax, double zmin, double zmax);
private:
std::vector<double> values;
int xsize, ysize, zsize;
double xmin, xmax, ymin, ymax, zmin, zmax;
};
/**
* This is a TabulatedFunction that computes a discrete one dimensional function f(x).
* To evaluate it, x is rounded to the nearest integer and the table element with that
* index is returned. If the index is outside the range [0, size), the result is undefined.
*/
class OPENMM_EXPORT Discrete1DFunction : public TabulatedFunction {
public:
/**
* Create a Discrete1DFunction f(x) based on a set of tabulated values.
*
* @param values the tabulated values of the function f(x)
*/
Discrete1DFunction(const std::vector<double>& values);
/**
* Get the parameters for the tabulated function.
*
* @param values the tabulated values of the function f(x)
*/
void getFunctionParameters(std::vector<double>& values) const;
/**
* Set the parameters for the tabulated function.
*
* @param values the tabulated values of the function f(x)
*/
void setFunctionParameters(const std::vector<double>& values);
private:
std::vector<double> values;
};
/**
* This is a TabulatedFunction that computes a discrete two dimensional function f(x,y).
* To evaluate it, x and y are each rounded to the nearest integer and the table element with those
* indices is returned. If either index is outside the range [0, size), the result is undefined.
*/
class OPENMM_EXPORT Discrete2DFunction : public TabulatedFunction {
public:
/**
* Create a Discrete2DFunction f(x,y) based on a set of tabulated values.
*
* @param xsize the number of table elements along the x direction
* @param ysize the number of table elements along the y direction
* @param values the tabulated values of the function f(x,y), ordered so that
* values[i+xsize*j] = f(i,j). This must be of length xsize*ysize.
*/
Discrete2DFunction(int xsize, int ysize, const std::vector<double>& values);
/**
* Get the parameters for the tabulated function.
*
* @param xsize the number of table elements along the x direction
* @param ysize the number of table elements along the y direction
* @param values the tabulated values of the function f(x,y), ordered so that
* values[i+xsize*j] = f(i,j). This must be of length xsize*ysize.
*/
void getFunctionParameters(int& xsize, int& ysize, std::vector<double>& values) const;
/**
* Set the parameters for the tabulated function.
*
* @param xsize the number of table elements along the x direction
* @param ysize the number of table elements along the y direction
* @param values the tabulated values of the function f(x,y), ordered so that
* values[i+xsize*j] = f(i,j). This must be of length xsize*ysize.
*/
void setFunctionParameters(int xsize, int ysize, const std::vector<double>& values);
private:
int xsize, ysize;
std::vector<double> values;
};
/**
* This is a TabulatedFunction that computes a discrete three dimensional function f(x,y,z).
* To evaluate it, x, y, and z are each rounded to the nearest integer and the table element with those
* indices is returned. If any index is outside the range [0, size), the result is undefined.
*/
class OPENMM_EXPORT Discrete3DFunction : public TabulatedFunction {
public:
/**
* Create a Discrete3DFunction f(x,y,z) based on a set of tabulated values.
*
* @param xsize the number of table elements along the x direction
* @param ysize the number of table elements along the y direction
* @param zsize the number of table elements along the z direction
* @param values the tabulated values of the function f(x,y,z), ordered so that
* values[i+xsize*j+xsize*ysize*k] = f(i,j,k). This must be of length xsize*ysize*zsize.
*/
Discrete3DFunction(int xsize, int ysize, int zsize, const std::vector<double>& values);
/**
* Get the parameters for the tabulated function.
*
* @param xsize the number of table elements along the x direction
* @param ysize the number of table elements along the y direction
* @param zsize the number of table elements along the z direction
* @param values the tabulated values of the function f(x,y,z), ordered so that
* values[i+xsize*j+xsize*ysize*k] = f(i,j,k). This must be of length xsize*ysize*zsize.
*/
void getFunctionParameters(int& xsize, int& ysize, int& zsize, std::vector<double>& values) const;
/**
* Set the parameters for the tabulated function.
*
* @param xsize the number of table elements along the x direction
* @param ysize the number of table elements along the y direction
* @param zsize the number of table elements along the z direction
* @param values the tabulated values of the function f(x,y,z), ordered so that
* values[i+xsize*j+xsize*ysize*k] = f(i,j,k). This must be of length xsize*ysize*zsize.
*/
void setFunctionParameters(int xsize, int ysize, int zsize, const std::vector<double>& values);
private:
int xsize, ysize, zsize;
std::vector<double> values;
};
} // namespace OpenMM
#endif /*OPENMM_TABULATEDFUNCTION_H_*/
openmmapi/include/openmm/internal/SplineFitter.h
View file @ cf8a03e8
......@@ -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/include/openmm/internal/ThreadPool.h
View file @ cf8a03e8
......@@ -53,7 +53,13 @@ class OPENMM_EXPORT ThreadPool {
public:
class Task;
class ThreadData;
ThreadPool();
/**
* Create a ThreadPool.
*
* @param numThreads the number of worker threads to create. If this is 0 (the default), the
* number of threads is set equal to the number of logical CPU cores available
*/
ThreadPool(int numThreads=0);
~ThreadPool();
/**
* Get the number of worker threads in the pool.
......
openmmapi/include/openmm/internal/vectorize8.h
View file @ cf8a03e8
......@@ -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) 2013 Stanford University and the Authors. *
* Portions copyright (c) 2013-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -201,13 +201,21 @@ static inline void transpose(const fvec4& in1, const fvec4& in2, const fvec4& in
fvec4 i5 = in5, i6 = in6, i7 = in7, i8 = in8;
_MM_TRANSPOSE4_PS(i1, i2, i3, i4);
_MM_TRANSPOSE4_PS(i5, i6, i7, i8);
#ifdef _MSC_VER
// Visual Studio has a bug in _mm256_castps128_ps256, so we have to use the more expensive _mm256_insertf128_ps.
out1 = _mm256_insertf128_ps(out1, i1, 0);
out2 = _mm256_insertf128_ps(out2, i2, 0);
out3 = _mm256_insertf128_ps(out3, i3, 0);
out4 = _mm256_insertf128_ps(out4, i4, 0);
#else
out1 = _mm256_castps128_ps256(i1);
out1 = _mm256_insertf128_ps(out1, i5, 1);
out2 = _mm256_castps128_ps256(i2);
out2 = _mm256_insertf128_ps(out2, i6, 1);
out3 = _mm256_castps128_ps256(i3);
out3 = _mm256_insertf128_ps(out3, i7, 1);
out4 = _mm256_castps128_ps256(i4);
#endif
out1 = _mm256_insertf128_ps(out1, i5, 1);
out2 = _mm256_insertf128_ps(out2, i6, 1);
out3 = _mm256_insertf128_ps(out3, i7, 1);
out4 = _mm256_insertf128_ps(out4, i8, 1);
}
......
openmmapi/src/CustomCompoundBondForce.cpp
View file @ cf8a03e8
......@@ -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 @ cf8a03e8
......@@ -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 @ cf8a03e8
......@@ -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 @ cf8a03e8
......@@ -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 @ cf8a03e8
......@@ -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) {
......
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