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Commit 708c4246 authored by Lee-Ping's avatar Lee-Ping
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Merge branch 'master' of github.com:SimTk/openmm

parents d284e2b8 ec90b4bb
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.travis.yml 0 → 100644
View file @ 708c4246
language: cpp
compiler:
- clang
before_install:
- sudo apt-get update -qq
- sudo apt-get install -qq libpcre3 libpcre3-dev gromacs
- sudo apt-get install -qq swig doxygen
- sudo apt-get install -qq python-numpy python-scipy python-nose
script:
- cmake -DCMAKE_INSTALL_PREFIX=~/OpenMM .
- make
- make test
- make install
- ls ~/OpenMM/include
- export LD_LIBRARY_PATH=~/OpenMM/lib/
- export OPENMM_LIB_PATH=~/OpenMM/lib/
- export OPENMM_INCLUDE_PATH=~/OpenMM/include/
- cd python
- sudo -E python setup.py install
- cd tests
- nosetests -vv
CMakeLists.txt
View file @ 708c4246
...@@ -87,8 +87,11 @@ IF(WIN32) ...@@ -87,8 +87,11 @@ IF(WIN32)
ENDFOREACH(lib) ENDFOREACH(lib)
LINK_DIRECTORIES("${CMAKE_CURRENT_BINARY_DIR}/${CMAKE_CFG_INTDIR}") LINK_DIRECTORIES("${CMAKE_CURRENT_BINARY_DIR}/${CMAKE_CFG_INTDIR}")
SET(PTHREADS_LIB pthreadVC2) SET(PTHREADS_LIB pthreadVC2)
SET(PTHREADS_LIB_STATIC pthreadVC2_static_mt)
ELSE(WIN32) ELSE(WIN32)
SET(PTHREADS_LIB pthread) SET(PTHREADS_LIB pthread)
# in linux, even in static builds we link against the dynamic object (since its tied to libc versions)
SET(PTHREADS_LIB_STATIC pthread)
ENDIF(WIN32) ENDIF(WIN32)
# The build system will set ARCH64 for 64 bit builds, which require # The build system will set ARCH64 for 64 bit builds, which require
......
README.md
View file @ 708c4246
## OpenMM: A High Performance Molecular Dynamics Library ## OpenMM: A High Performance Molecular Dynamics Library
[![Build Status](https://travis-ci.org/SimTk/openmm.png?branch=master)](https://travis-ci.org/SimTk/openmm)
Introduction Introduction
------------ ------------
......
openmmapi/include/OpenMM.h
View file @ 708c4246
...@@ -62,6 +62,7 @@ ...@@ -62,6 +62,7 @@
#include "openmm/RBTorsionForce.h" #include "openmm/RBTorsionForce.h"
#include "openmm/State.h" #include "openmm/State.h"
#include "openmm/System.h" #include "openmm/System.h"
#include "openmm/TabulatedFunction.h"
#include "openmm/Units.h" #include "openmm/Units.h"
#include "openmm/VariableLangevinIntegrator.h" #include "openmm/VariableLangevinIntegrator.h"
#include "openmm/VariableVerletIntegrator.h" #include "openmm/VariableVerletIntegrator.h"
......
openmmapi/include/openmm/CustomCompoundBondForce.h
View file @ 708c4246
...@@ -9,7 +9,7 @@ ...@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * 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 * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -32,6 +32,7 @@ ...@@ -32,6 +32,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. * * USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include "TabulatedFunction.h"
#include "Force.h" #include "Force.h"
#include "Vec3.h" #include "Vec3.h"
#include <vector> #include <vector>
...@@ -91,8 +92,8 @@ namespace OpenMM { ...@@ -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 * 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. * 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 * In addition, you can call addTabulatedFunction() to define a new function based on tabulated values. You specify the function by
* values, and a natural spline is created from them. That function can then appear in the expression. * creating a TabulatedFunction object. That function can then appear in the expression.
*/ */
class OPENMM_EXPORT CustomCompoundBondForce : public Force { class OPENMM_EXPORT CustomCompoundBondForce : public Force {
...@@ -106,6 +107,7 @@ public: ...@@ -106,6 +107,7 @@ public:
* and per-bond parameters * and per-bond parameters
*/ */
explicit CustomCompoundBondForce(int numParticles, const std::string& energy); explicit CustomCompoundBondForce(int numParticles, const std::string& energy);
~CustomCompoundBondForce();
/** /**
* Get the number of particles used to define each bond. * Get the number of particles used to define each bond.
*/ */
...@@ -133,6 +135,14 @@ public: ...@@ -133,6 +135,14 @@ public:
/** /**
* Get the number of tabulated functions that have been defined. * 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 { int getNumFunctions() const {
return functions.size(); return functions.size();
} }
...@@ -229,33 +239,51 @@ public: ...@@ -229,33 +239,51 @@ public:
* Add a tabulated function that may appear in the energy expression. * Add a tabulated function that may appear in the energy expression.
* *
* @param name the name of the function as it appears 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. * @param function a TabulatedFunction object defining the function. The TabulatedFunction
* The function is assumed to be zero for x &lt; min or x &gt; max. * should have been created on the heap with the "new" operator. The
* @param min the value of the independent variable corresponding to the first element of values * Force takes over ownership of it, and deletes it when the Force itself is deleted.
* @param max the value of the independent variable corresponding to the last element of values
* @return the index of the function that was added * @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); 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 the energy expression.
* *
* @param index the index of the function for which to get parameters * @deprecated This method exists only for backward compatibility. Use getTabulatedFunctionParameters() instead.
* @param name the name of the function as it appears in expressions * If the specified function is not a Continuous1DFunction, this throws an exception.
* @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
*/ */
void getFunctionParameters(int index, std::string& name, std::vector<double>& values, double& min, double& max) const; 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 * @deprecated This method exists only for backward compatibility. Use setTabulatedFunctionParameters() instead.
* @param name the name of the function as it appears in expressions * If the specified function is not a Continuous1DFunction, this throws an exception.
* @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
*/ */
void setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double max); void setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double max);
/** /**
...@@ -333,12 +361,10 @@ public: ...@@ -333,12 +361,10 @@ public:
class CustomCompoundBondForce::FunctionInfo { class CustomCompoundBondForce::FunctionInfo {
public: public:
std::string name; std::string name;
std::vector<double> values; TabulatedFunction* function;
double min, max;
FunctionInfo() { FunctionInfo() {
} }
FunctionInfo(const std::string& name, const std::vector<double>& values, double min, double max) : FunctionInfo(const std::string& name, TabulatedFunction* function) : name(name), function(function) {
name(name), values(values), min(min), max(max) {
} }
}; };
......
openmmapi/include/openmm/CustomGBForce.h
View file @ 708c4246
...@@ -9,7 +9,7 @@ ...@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * 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 * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -32,6 +32,7 @@ ...@@ -32,6 +32,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. * * USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include "TabulatedFunction.h"
#include "Force.h" #include "Force.h"
#include "Vec3.h" #include "Vec3.h"
#include <map> #include <map>
...@@ -134,8 +135,8 @@ namespace OpenMM { ...@@ -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, * 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. * 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 * In addition, you can call addTabulatedFunction() to define a new function based on tabulated values. You specify the function by
* values, and a natural spline is created from them. That function can then appear in expressions. * creating a TabulatedFunction object. That function can then appear in expressions.
*/ */
class OPENMM_EXPORT CustomGBForce : public Force { class OPENMM_EXPORT CustomGBForce : public Force {
...@@ -181,6 +182,7 @@ public: ...@@ -181,6 +182,7 @@ public:
* Create a CustomGBForce. * Create a CustomGBForce.
*/ */
CustomGBForce(); CustomGBForce();
~CustomGBForce();
/** /**
* Get the number of particles for which force field parameters have been defined. * Get the number of particles for which force field parameters have been defined.
*/ */
...@@ -208,6 +210,14 @@ public: ...@@ -208,6 +210,14 @@ public:
/** /**
* Get the number of tabulated functions that have been defined. * 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 { int getNumFunctions() const {
return functions.size(); return functions.size();
} }
...@@ -452,36 +462,54 @@ public: ...@@ -452,36 +462,54 @@ public:
*/ */
void setExclusionParticles(int index, int particle1, int particle2); 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 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. * @param function a TabulatedFunction object defining the function. The TabulatedFunction
* The function is assumed to be zero for x &lt; min or x &gt; max. * should have been created on the heap with the "new" operator. The
* @param min the value of the independent variable corresponding to the first element of values * Force takes over ownership of it, and deletes it when the Force itself is deleted.
* @param max the value of the independent variable corresponding to the last element of values
* @return the index of the function that was added * @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); 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 * @deprecated This method exists only for backward compatibility. Use getTabulatedFunctionParameters() instead.
* @param name the name of the function as it appears in expressions * If the specified function is not a Continuous1DFunction, this throws an exception.
* @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
*/ */
void getFunctionParameters(int index, std::string& name, std::vector<double>& values, double& min, double& max) const; 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 * @deprecated This method exists only for backward compatibility. Use setTabulatedFunctionParameters() instead.
* @param name the name of the function as it appears in expressions * If the specified function is not a Continuous1DFunction, this throws an exception.
* @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
*/ */
void setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double max); void setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double max);
/** /**
...@@ -577,12 +605,10 @@ public: ...@@ -577,12 +605,10 @@ public:
class CustomGBForce::FunctionInfo { class CustomGBForce::FunctionInfo {
public: public:
std::string name; std::string name;
std::vector<double> values; TabulatedFunction* function;
double min, max;
FunctionInfo() { FunctionInfo() {
} }
FunctionInfo(const std::string& name, const std::vector<double>& values, double min, double max) : FunctionInfo(const std::string& name, TabulatedFunction* function) : name(name), function(function) {
name(name), values(values), min(min), max(max) {
} }
}; };
......
openmmapi/include/openmm/CustomHbondForce.h
View file @ 708c4246
...@@ -9,7 +9,7 @@ ...@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * 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 * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -32,6 +32,7 @@ ...@@ -32,6 +32,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. * * USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include "TabulatedFunction.h"
#include "Force.h" #include "Force.h"
#include "Vec3.h" #include "Vec3.h"
#include <map> #include <map>
...@@ -91,8 +92,8 @@ namespace OpenMM { ...@@ -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 * 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. * 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 * In addition, you can call addTabulatedFunction() to define a new function based on tabulated values. You specify the function by
* values, and a natural spline is created from them. That function can then appear in the expression. * creating a TabulatedFunction object. That function can then appear in the expression.
*/ */
class OPENMM_EXPORT CustomHbondForce : public Force { class OPENMM_EXPORT CustomHbondForce : public Force {
...@@ -124,6 +125,7 @@ public: ...@@ -124,6 +125,7 @@ public:
* per-acceptor parameters * per-acceptor parameters
*/ */
explicit CustomHbondForce(const std::string& energy); explicit CustomHbondForce(const std::string& energy);
~CustomHbondForce();
/** /**
* Get the number of donors for which force field parameters have been defined. * Get the number of donors for which force field parameters have been defined.
*/ */
...@@ -163,6 +165,14 @@ public: ...@@ -163,6 +165,14 @@ public:
/** /**
* Get the number of tabulated functions that have been defined. * 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 { int getNumFunctions() const {
return functions.size(); return functions.size();
} }
...@@ -374,33 +384,51 @@ public: ...@@ -374,33 +384,51 @@ public:
* Add a tabulated function that may appear in the energy expression. * Add a tabulated function that may appear in the energy expression.
* *
* @param name the name of the function as it appears 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. * @param function a TabulatedFunction object defining the function. The TabulatedFunction
* The function is assumed to be zero for x &lt; min or x &gt; max. * should have been created on the heap with the "new" operator. The
* @param min the value of the independent variable corresponding to the first element of values * Force takes over ownership of it, and deletes it when the Force itself is deleted.
* @param max the value of the independent variable corresponding to the last element of values
* @return the index of the function that was added * @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); 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 the energy expression.
* *
* @param index the index of the function for which to get parameters * @deprecated This method exists only for backward compatibility. Use getTabulatedFunctionParameters() instead.
* @param name the name of the function as it appears in expressions * If the specified function is not a Continuous1DFunction, this throws an exception.
* @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
*/ */
void getFunctionParameters(int index, std::string& name, std::vector<double>& values, double& min, double& max) const; 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 * @deprecated This method exists only for backward compatibility. Use setTabulatedFunctionParameters() instead.
* @param name the name of the function as it appears in expressions * If the specified function is not a Continuous1DFunction, this throws an exception.
* @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
*/ */
void setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double max); void setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double max);
/** /**
...@@ -499,12 +527,10 @@ public: ...@@ -499,12 +527,10 @@ public:
class CustomHbondForce::FunctionInfo { class CustomHbondForce::FunctionInfo {
public: public:
std::string name; std::string name;
std::vector<double> values; TabulatedFunction* function;
double min, max;
FunctionInfo() { FunctionInfo() {
} }
FunctionInfo(const std::string& name, const std::vector<double>& values, double min, double max) : FunctionInfo(const std::string& name, TabulatedFunction* function) : name(name), function(function) {
name(name), values(values), min(min), max(max) {
} }
}; };
......
openmmapi/include/openmm/CustomNonbondedForce.h
View file @ 708c4246
...@@ -9,7 +9,7 @@ ...@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * 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 * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -32,6 +32,7 @@ ...@@ -32,6 +32,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. * * USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include "TabulatedFunction.h"
#include "Force.h" #include "Force.h"
#include "Vec3.h" #include "Vec3.h"
#include <map> #include <map>
...@@ -124,8 +125,8 @@ namespace OpenMM { ...@@ -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, * 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. * 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 * In addition, you can call addTabulatedFunction() to define a new function based on tabulated values. You specify the function by
* values, and a natural spline is created from them. That function can then appear in the expression. * creating a TabulatedFunction object. That function can then appear in the expression.
*/ */
class OPENMM_EXPORT CustomNonbondedForce : public Force { class OPENMM_EXPORT CustomNonbondedForce : public Force {
...@@ -156,6 +157,7 @@ public: ...@@ -156,6 +157,7 @@ public:
* of r, the distance between them, as well as any global and per-particle parameters * of r, the distance between them, as well as any global and per-particle parameters
*/ */
explicit CustomNonbondedForce(const std::string& energy); explicit CustomNonbondedForce(const std::string& energy);
~CustomNonbondedForce();
/** /**
* Get the number of particles for which force field parameters have been defined. * Get the number of particles for which force field parameters have been defined.
*/ */
...@@ -183,6 +185,14 @@ public: ...@@ -183,6 +185,14 @@ public:
/** /**
* Get the number of tabulated functions that have been defined. * 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 { int getNumFunctions() const {
return functions.size(); return functions.size();
} }
...@@ -359,33 +369,51 @@ public: ...@@ -359,33 +369,51 @@ public:
* Add a tabulated function that may appear in the energy expression. * Add a tabulated function that may appear in the energy expression.
* *
* @param name the name of the function as it appears 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. * @param function a TabulatedFunction object defining the function. The TabulatedFunction
* The function is assumed to be zero for x &lt; min or x &gt; max. * should have been created on the heap with the "new" operator. The
* @param min the value of the independent variable corresponding to the first element of values * Force takes over ownership of it, and deletes it when the Force itself is deleted.
* @param max the value of the independent variable corresponding to the last element of values
* @return the index of the function that was added * @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); 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 the energy expression.
* *
* @param index the index of the function for which to get parameters * @deprecated This method exists only for backward compatibility. Use getTabulatedFunctionParameters() instead.
* @param name the name of the function as it appears in expressions * If the specified function is not a Continuous1DFunction, this throws an exception.
* @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
*/ */
void getFunctionParameters(int index, std::string& name, std::vector<double>& values, double& min, double& max) const; 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 * @deprecated This method exists only for backward compatibility. Use setTabulatedFunctionParameters() instead.
* @param name the name of the function as it appears in expressions * If the specified function is not a Continuous1DFunction, this throws an exception.
* @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
*/ */
void setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double max); void setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double max);
/** /**
...@@ -507,12 +535,10 @@ public: ...@@ -507,12 +535,10 @@ public:
class CustomNonbondedForce::FunctionInfo { class CustomNonbondedForce::FunctionInfo {
public: public:
std::string name; std::string name;
std::vector<double> values; TabulatedFunction* function;
double min, max;
FunctionInfo() { FunctionInfo() {
} }
FunctionInfo(const std::string& name, const std::vector<double>& values, double min, double max) : FunctionInfo(const std::string& name, TabulatedFunction* function) : name(name), function(function) {
name(name), values(values), min(min), max(max) {
} }
}; };
......
openmmapi/include/openmm/TabulatedFunction.h 0 → 100644
View file @ 708c4246
This diff is collapsed.
openmmapi/include/openmm/internal/SplineFitter.h
View file @ 708c4246
...@@ -9,7 +9,7 @@ ...@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * 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 * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -67,7 +67,7 @@ public: ...@@ -67,7 +67,7 @@ public:
*/ */
static void createPeriodicSpline(const std::vector<double>& x, const std::vector<double>& y, std::vector<double>& deriv); 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 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 * @param y the values of the dependent variable at the data points to interpolate
...@@ -77,7 +77,7 @@ public: ...@@ -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); 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 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 * @param y the values of the dependent variable at the data points to interpolate
...@@ -86,6 +86,90 @@ public: ...@@ -86,6 +86,90 @@ public:
* @return the value of the spline's derivative at the specified point * @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); 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: 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); static void solveTridiagonalMatrix(const std::vector<double>& a, const std::vector<double>& b, const std::vector<double>& c, const std::vector<double>& rhs, std::vector<double>& sol);
}; };
......
openmmapi/src/CustomCompoundBondForce.cpp
View file @ 708c4246
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * 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 * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -51,6 +51,12 @@ using std::vector; ...@@ -51,6 +51,12 @@ using std::vector;
CustomCompoundBondForce::CustomCompoundBondForce(int numParticles, const string& energy) : particlesPerBond(numParticles), energyExpression(energy) { 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 { const string& CustomCompoundBondForce::getEnergyFunction() const {
return energyExpression; return energyExpression;
} }
...@@ -120,33 +126,47 @@ void CustomCompoundBondForce::setBondParameters(int index, const vector<int>& pa ...@@ -120,33 +126,47 @@ void CustomCompoundBondForce::setBondParameters(int index, const vector<int>& pa
bonds[index].parameters = parameters; 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) { int CustomCompoundBondForce::addFunction(const std::string& name, const std::vector<double>& values, double min, double max) {
if (max <= min) functions.push_back(FunctionInfo(name, new Continuous1DFunction(values, min, max)));
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));
return functions.size()-1; return functions.size()-1;
} }
void CustomCompoundBondForce::getFunctionParameters(int index, std::string& name, std::vector<double>& values, double& min, double& max) const { void CustomCompoundBondForce::getFunctionParameters(int index, std::string& name, std::vector<double>& values, double& min, double& max) const {
ASSERT_VALID_INDEX(index, functions); 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; name = functions[index].name;
values = functions[index].values; function->getFunctionParameters(values, min, max);
min = functions[index].min;
max = functions[index].max;
} }
void CustomCompoundBondForce::setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double 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); 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].name = name;
functions[index].values = values; function->setFunctionParameters(values, min, max);
functions[index].min = min;
functions[index].max = max;
} }
ForceImpl* CustomCompoundBondForce::createImpl() const { ForceImpl* CustomCompoundBondForce::createImpl() const {
......
openmmapi/src/CustomCompoundBondForceImpl.cpp
View file @ 708c4246
...@@ -147,7 +147,7 @@ ParsedExpression CustomCompoundBondForceImpl::prepareExpression(const CustomComp ...@@ -147,7 +147,7 @@ ParsedExpression CustomCompoundBondForceImpl::prepareExpression(const CustomComp
ExpressionTreeNode CustomCompoundBondForceImpl::replaceFunctions(const ExpressionTreeNode& node, map<string, int> atoms, 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) { map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals) {
const Operation& op = node.getOperation(); 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. // This is not an angle or dihedral, so process its children.
......
openmmapi/src/CustomGBForce.cpp
View file @ 708c4246
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * 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 * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -50,6 +50,11 @@ using std::vector; ...@@ -50,6 +50,11 @@ using std::vector;
CustomGBForce::CustomGBForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0) { 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 { CustomGBForce::NonbondedMethod CustomGBForce::getNonbondedMethod() const {
return nonbondedMethod; return nonbondedMethod;
} }
...@@ -173,33 +178,47 @@ void CustomGBForce::setExclusionParticles(int index, int particle1, int particle ...@@ -173,33 +178,47 @@ void CustomGBForce::setExclusionParticles(int index, int particle1, int particle
exclusions[index].particle2 = particle2; 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) { int CustomGBForce::addFunction(const std::string& name, const std::vector<double>& values, double min, double max) {
if (max <= min) functions.push_back(FunctionInfo(name, new Continuous1DFunction(values, min, max)));
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));
return functions.size()-1; return functions.size()-1;
} }
void CustomGBForce::getFunctionParameters(int index, std::string& name, std::vector<double>& values, double& min, double& max) const { void CustomGBForce::getFunctionParameters(int index, std::string& name, std::vector<double>& values, double& min, double& max) const {
ASSERT_VALID_INDEX(index, functions); 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; name = functions[index].name;
values = functions[index].values; function->getFunctionParameters(values, min, max);
min = functions[index].min;
max = functions[index].max;
} }
void CustomGBForce::setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double 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); 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].name = name;
functions[index].values = values; function->setFunctionParameters(values, min, max);
functions[index].min = min;
functions[index].max = max;
} }
ForceImpl* CustomGBForce::createImpl() const { ForceImpl* CustomGBForce::createImpl() const {
......
openmmapi/src/CustomHbondForce.cpp
View file @ 708c4246
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * 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 * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -50,6 +50,12 @@ using std::vector; ...@@ -50,6 +50,12 @@ using std::vector;
CustomHbondForce::CustomHbondForce(const string& energy) : energyExpression(energy), nonbondedMethod(NoCutoff), cutoffDistance(1.0) { 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 { const string& CustomHbondForce::getEnergyFunction() const {
return energyExpression; return energyExpression;
} }
...@@ -187,33 +193,47 @@ void CustomHbondForce::setExclusionParticles(int index, int donor, int acceptor) ...@@ -187,33 +193,47 @@ void CustomHbondForce::setExclusionParticles(int index, int donor, int acceptor)
exclusions[index].acceptor = 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) { int CustomHbondForce::addFunction(const std::string& name, const std::vector<double>& values, double min, double max) {
if (max <= min) functions.push_back(FunctionInfo(name, new Continuous1DFunction(values, min, max)));
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));
return functions.size()-1; return functions.size()-1;
} }
void CustomHbondForce::getFunctionParameters(int index, std::string& name, std::vector<double>& values, double& min, double& max) const { void CustomHbondForce::getFunctionParameters(int index, std::string& name, std::vector<double>& values, double& min, double& max) const {
ASSERT_VALID_INDEX(index, functions); 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; name = functions[index].name;
values = functions[index].values; function->getFunctionParameters(values, min, max);
min = functions[index].min;
max = functions[index].max;
} }
void CustomHbondForce::setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double 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); 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].name = name;
functions[index].values = values; function->setFunctionParameters(values, min, max);
functions[index].min = min;
functions[index].max = max;
} }
ForceImpl* CustomHbondForce::createImpl() const { ForceImpl* CustomHbondForce::createImpl() const {
......
openmmapi/src/CustomNonbondedForce.cpp
View file @ 708c4246
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * 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 * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -51,6 +51,11 @@ CustomNonbondedForce::CustomNonbondedForce(const string& energy) : energyExpress ...@@ -51,6 +51,11 @@ CustomNonbondedForce::CustomNonbondedForce(const string& energy) : energyExpress
switchingDistance(-1.0), useSwitchingFunction(false), useLongRangeCorrection(false) { 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 { const string& CustomNonbondedForce::getEnergyFunction() const {
return energyExpression; return energyExpression;
} }
...@@ -169,34 +174,47 @@ void CustomNonbondedForce::setExclusionParticles(int index, int particle1, int p ...@@ -169,34 +174,47 @@ void CustomNonbondedForce::setExclusionParticles(int index, int particle1, int p
exclusions[index].particle1 = particle1; exclusions[index].particle1 = particle1;
exclusions[index].particle2 = particle2; 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) { int CustomNonbondedForce::addFunction(const std::string& name, const std::vector<double>& values, double min, double max) {
if (max <= min) functions.push_back(FunctionInfo(name, new Continuous1DFunction(values, min, max)));
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));
return functions.size()-1; return functions.size()-1;
} }
void CustomNonbondedForce::getFunctionParameters(int index, std::string& name, std::vector<double>& values, double& min, double& max) const { void CustomNonbondedForce::getFunctionParameters(int index, std::string& name, std::vector<double>& values, double& min, double& max) const {
ASSERT_VALID_INDEX(index, functions); 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; name = functions[index].name;
values = functions[index].values; function->getFunctionParameters(values, min, max);
min = functions[index].min;
max = functions[index].max;
} }
void CustomNonbondedForce::setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double 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); 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].name = name;
functions[index].values = values; function->setFunctionParameters(values, min, max);
functions[index].min = min;
functions[index].max = max;
} }
int CustomNonbondedForce::addInteractionGroup(const std::set<int>& set1, const std::set<int>& set2) { int CustomNonbondedForce::addInteractionGroup(const std::set<int>& set1, const std::set<int>& set2) {
......
openmmapi/src/SplineFitter.cpp
View file @ 708c4246
This diff is collapsed.
openmmapi/src/TabulatedFunction.cpp 0 → 100644
View file @ 708c4246
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/TabulatedFunction.h"
#include "openmm/OpenMMException.h"
using namespace OpenMM;
using namespace std;
Continuous1DFunction::Continuous1DFunction(const vector<double>& values, double min, double max) {
if (max <= min)
throw OpenMMException("Continuous1DFunction: max <= min for a tabulated function.");
if (values.size() < 2)
throw OpenMMException("Continuous1DFunction: a tabulated function must have at least two points");
this->values = values;
this->min = min;
this->max = max;
}
void Continuous1DFunction::getFunctionParameters(vector<double>& values, double& min, double& max) const {
values = this->values;
min = this->min;
max = this->max;
}
void Continuous1DFunction::setFunctionParameters(const vector<double>& values, double min, double max) {
if (max <= min)
throw OpenMMException("Continuous1DFunction: max <= min for a tabulated function.");
if (values.size() < 2)
throw OpenMMException("Continuous1DFunction: a tabulated function must have at least two points");
this->values = values;
this->min = min;
this->max = max;
}
Continuous2DFunction::Continuous2DFunction(int xsize, int ysize, const vector<double>& values, double xmin, double xmax, double ymin, double ymax) {
if (xsize < 2 || ysize < 2)
throw OpenMMException("Continuous2DFunction: must have at least two points along each axis");
if (values.size() != xsize*ysize)
throw OpenMMException("Continuous2DFunction: incorrect number of values");
if (xmax <= xmin)
throw OpenMMException("Continuous2DFunction: xmax <= xmin for a tabulated function.");
if (ymax <= ymin)
throw OpenMMException("Continuous2DFunction: ymax <= ymin for a tabulated function.");
this->values = values;
this->xsize = xsize;
this->ysize = ysize;
this->xmin = xmin;
this->xmax = xmax;
this->ymin = ymin;
this->ymax = ymax;
}
void Continuous2DFunction::getFunctionParameters(int& xsize, int& ysize, vector<double>& values, double& xmin, double& xmax, double& ymin, double& ymax) const {
values = this->values;
xsize = this->xsize;
ysize = this->ysize;
xmin = this->xmin;
xmax = this->xmax;
ymin = this->ymin;
ymax = this->ymax;
}
void Continuous2DFunction::setFunctionParameters(int xsize, int ysize, const vector<double>& values, double xmin, double xmax, double ymin, double ymax) {
if (xsize < 2 || ysize < 2)
throw OpenMMException("Continuous2DFunction: must have at least two points along each axis");
if (values.size() != xsize*ysize)
throw OpenMMException("Continuous2DFunction: incorrect number of values");
if (xmax <= xmin)
throw OpenMMException("Continuous2DFunction: xmax <= xmin for a tabulated function.");
if (ymax <= ymin)
throw OpenMMException("Continuous2DFunction: ymax <= ymin for a tabulated function.");
this->values = values;
this->xsize = xsize;
this->ysize = ysize;
this->xmin = xmin;
this->xmax = xmax;
this->ymin = ymin;
this->ymax = ymax;
}
Continuous3DFunction::Continuous3DFunction(int xsize, int ysize, int zsize, const vector<double>& values, double xmin, double xmax, double ymin, double ymax, double zmin, double zmax) {
if (xsize < 2 || ysize < 2 || zsize < 2)
throw OpenMMException("Continuous3DFunction: must have at least two points along each axis");
if (values.size() != xsize*ysize*zsize)
throw OpenMMException("Continuous3DFunction: incorrect number of values");
if (xmax <= xmin)
throw OpenMMException("Continuous3DFunction: xmax <= xmin for a tabulated function.");
if (ymax <= ymin)
throw OpenMMException("Continuous3DFunction: ymax <= ymin for a tabulated function.");
if (zmax <= zmin)
throw OpenMMException("Continuous3DFunction: zmax <= zmin for a tabulated function.");
this->values = values;
this->xsize = xsize;
this->ysize = ysize;
this->zsize = zsize;
this->xmin = xmin;
this->xmax = xmax;
this->ymin = ymin;
this->ymax = ymax;
this->zmin = zmin;
this->zmax = zmax;
}
void Continuous3DFunction::getFunctionParameters(int& xsize, int& ysize, int& zsize, vector<double>& values, double& xmin, double& xmax, double& ymin, double& ymax, double& zmin, double& zmax) const {
values = this->values;
xsize = this->xsize;
ysize = this->ysize;
zsize = this->zsize;
xmin = this->xmin;
xmax = this->xmax;
ymin = this->ymin;
ymax = this->ymax;
zmin = this->zmin;
zmax = this->zmax;
}
void Continuous3DFunction::setFunctionParameters(int xsize, int ysize, int zsize, const vector<double>& values, double xmin, double xmax, double ymin, double ymax, double zmin, double zmax) {
if (xsize < 2 || ysize < 2 || zsize < 2)
throw OpenMMException("Continuous3DFunction: must have at least two points along each axis");
if (values.size() != xsize*ysize*zsize)
throw OpenMMException("Continuous3DFunction: incorrect number of values");
if (xmax <= xmin)
throw OpenMMException("Continuous3DFunction: xmax <= xmin for a tabulated function.");
if (ymax <= ymin)
throw OpenMMException("Continuous3DFunction: ymax <= ymin for a tabulated function.");
if (zmax <= zmin)
throw OpenMMException("Continuous3DFunction: zmax <= zmin for a tabulated function.");
this->values = values;
this->xsize = xsize;
this->ysize = ysize;
this->zsize = zsize;
this->xmin = xmin;
this->xmax = xmax;
this->ymin = ymin;
this->ymax = ymax;
this->zmin = zmin;
this->zmax = zmax;
}
Discrete1DFunction::Discrete1DFunction(const vector<double>& values) {
this->values = values;
}
void Discrete1DFunction::getFunctionParameters(vector<double>& values) const {
values = this->values;
}
void Discrete1DFunction::setFunctionParameters(const vector<double>& values) {
this->values = values;
}
Discrete2DFunction::Discrete2DFunction(int xsize, int ysize, const vector<double>& values) {
if (values.size() != xsize*ysize)
throw OpenMMException("Discrete2DFunction: incorrect number of values");
this->xsize = xsize;
this->ysize = ysize;
this->values = values;
}
void Discrete2DFunction::getFunctionParameters(int& xsize, int& ysize, vector<double>& values) const {
xsize = this->xsize;
ysize = this->ysize;
values = this->values;
}
void Discrete2DFunction::setFunctionParameters(int xsize, int ysize, const vector<double>& values) {
if (values.size() != xsize*ysize)
throw OpenMMException("Discrete2DFunction: incorrect number of values");
this->xsize = xsize;
this->ysize = ysize;
this->values = values;
}
Discrete3DFunction::Discrete3DFunction(int xsize, int ysize, int zsize, const vector<double>& values) {
if (values.size() != xsize*ysize*zsize)
throw OpenMMException("Discrete3DFunction: incorrect number of values");
this->xsize = xsize;
this->ysize = ysize;
this->zsize = zsize;
this->values = values;
}
void Discrete3DFunction::getFunctionParameters(int& xsize, int& ysize, int& zsize, vector<double>& values) const {
xsize = this->xsize;
ysize = this->ysize;
zsize = this->zsize;
values = this->values;
}
void Discrete3DFunction::setFunctionParameters(int xsize, int ysize, int zsize, const vector<double>& values) {
if (values.size() != xsize*ysize*zsize)
throw OpenMMException("Discrete3DFunction: incorrect number of values");
this->xsize = xsize;
this->ysize = ysize;
this->zsize = zsize;
this->values = values;
}
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