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Commit 75a04e7f authored by peastman's avatar peastman
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Renamed methods for dealing with TabulatedFunctions to avoid problems in... 

Renamed methods for dealing with TabulatedFunctions to avoid problems in wrapper APIs.  Also fixed a few bugs.
parent f7e5492d
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openmmapi/include/openmm/CustomCompoundBondForce.h
View file @ 75a04e7f
......@@ -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: *
* *
......@@ -92,7 +92,7 @@ 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 the function by
* 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.
*/
......@@ -135,6 +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();
}
......@@ -236,49 +244,46 @@ public:
* Force takes over ownership of it, and deletes it when the Force itself is deleted.
* @return the index of the function that was added
*/
int addFunction(const std::string& name, TabulatedFunction* function);
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& getFunction(int index) const;
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& getFunction(int index);
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& getFunctionName(int index) const;
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 the version that takes
* a TabulatedFunction instead.
* @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.
*
* @deprecated This method exists only for backward compatibility. Use the version that takes
* a TabulatedFunction instead. If the specified function is not a Continuous1DFunction, this throws
* an exception.
* @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 the energy expression.
*
* @deprecated This method exists only for backward compatibility. Use the version that takes
* a TabulatedFunction instead. If the specified function is not a Continuous1DFunction, this throws
* an exception.
* @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);
/**
......
openmmapi/include/openmm/CustomGBForce.h
View file @ 75a04e7f
......@@ -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: *
* *
......@@ -135,7 +135,7 @@ 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 the function by
* 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.
*/
......@@ -210,6 +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();
}
......@@ -462,49 +470,46 @@ public:
* Force takes over ownership of it, and deletes it when the Force itself is deleted.
* @return the index of the function that was added
*/
int addFunction(const std::string& name, TabulatedFunction* function);
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& getFunction(int index) const;
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& getFunction(int index);
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& getFunctionName(int index) const;
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 the version that takes
* a TabulatedFunction instead.
* @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 expressions.
*
* @deprecated This method exists only for backward compatibility. Use the version that takes
* a TabulatedFunction instead. If the specified function is not a Continuous1DFunction, this throws
* an exception.
* @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 expressions.
*
* @deprecated This method exists only for backward compatibility. Use the version that takes
* a TabulatedFunction instead. If the specified function is not a Continuous1DFunction, this throws
* an exception.
* @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);
/**
......
openmmapi/include/openmm/CustomHbondForce.h
View file @ 75a04e7f
......@@ -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: *
* *
......@@ -92,7 +92,7 @@ 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 the function by
* 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.
*/
......@@ -165,6 +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();
}
......@@ -381,49 +389,46 @@ public:
* Force takes over ownership of it, and deletes it when the Force itself is deleted.
* @return the index of the function that was added
*/
int addFunction(const std::string& name, TabulatedFunction* function);
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& getFunction(int index) const;
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& getFunction(int index);
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& getFunctionName(int index) const;
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 the version that takes
* a TabulatedFunction instead.
* @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.
*
* @deprecated This method exists only for backward compatibility. Use the version that takes
* a TabulatedFunction instead. If the specified function is not a Continuous1DFunction, this throws
* an exception.
* @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 the energy expression.
*
* @deprecated This method exists only for backward compatibility. Use the version that takes
* a TabulatedFunction instead. If the specified function is not a Continuous1DFunction, this throws
* an exception.
* @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);
/**
......
openmmapi/include/openmm/CustomNonbondedForce.h
View file @ 75a04e7f
......@@ -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: *
* *
......@@ -125,7 +125,7 @@ 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 the function by
* 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.
*/
......@@ -185,6 +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();
}
......@@ -366,49 +374,46 @@ public:
* Force takes over ownership of it, and deletes it when the Force itself is deleted.
* @return the index of the function that was added
*/
int addFunction(const std::string& name, TabulatedFunction* function);
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& getFunction(int index) const;
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& getFunction(int index);
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& getFunctionName(int index) const;
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 the version that takes
* a TabulatedFunction instead.
* @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.
*
* @deprecated This method exists only for backward compatibility. Use the version that takes
* a TabulatedFunction instead. If the specified function is not a Continuous1DFunction, this throws
* an exception.
* @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 the energy expression.
*
* @deprecated This method exists only for backward compatibility. Use the version that takes
* a TabulatedFunction instead. If the specified function is not a Continuous1DFunction, this throws
* an exception.
* @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);
/**
......
openmmapi/src/CustomCompoundBondForce.cpp
View file @ 75a04e7f
......@@ -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: *
* *
......@@ -126,22 +126,22 @@ void CustomCompoundBondForce::setBondParameters(int index, const vector<int>& pa
bonds[index].parameters = parameters;
}
int CustomCompoundBondForce::addFunction(const std::string& name, TabulatedFunction* function) {
int CustomCompoundBondForce::addTabulatedFunction(const std::string& name, TabulatedFunction* function) {
functions.push_back(FunctionInfo(name, function));
return functions.size()-1;
}
const TabulatedFunction& CustomCompoundBondForce::getFunction(int index) const {
const TabulatedFunction& CustomCompoundBondForce::getTabulatedFunction(int index) const {
ASSERT_VALID_INDEX(index, functions);
return *functions[index].function;
}
TabulatedFunction& CustomCompoundBondForce::getFunction(int index) {
TabulatedFunction& CustomCompoundBondForce::getTabulatedFunction(int index) {
ASSERT_VALID_INDEX(index, functions);
return *functions[index].function;
}
const string& CustomCompoundBondForce::getFunctionName(int index) const {
const string& CustomCompoundBondForce::getTabulatedFunctionName(int index) const {
ASSERT_VALID_INDEX(index, functions);
return functions[index].name;
}
......
openmmapi/src/CustomGBForce.cpp
View file @ 75a04e7f
......@@ -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: *
* *
......@@ -178,22 +178,22 @@ void CustomGBForce::setExclusionParticles(int index, int particle1, int particle
exclusions[index].particle2 = particle2;
}
int CustomGBForce::addFunction(const std::string& name, TabulatedFunction* function) {
int CustomGBForce::addTabulatedFunction(const std::string& name, TabulatedFunction* function) {
functions.push_back(FunctionInfo(name, function));
return functions.size()-1;
}
const TabulatedFunction& CustomGBForce::getFunction(int index) const {
const TabulatedFunction& CustomGBForce::getTabulatedFunction(int index) const {
ASSERT_VALID_INDEX(index, functions);
return *functions[index].function;
}
TabulatedFunction& CustomGBForce::getFunction(int index) {
TabulatedFunction& CustomGBForce::getTabulatedFunction(int index) {
ASSERT_VALID_INDEX(index, functions);
return *functions[index].function;
}
const string& CustomGBForce::getFunctionName(int index) const {
const string& CustomGBForce::getTabulatedFunctionName(int index) const {
ASSERT_VALID_INDEX(index, functions);
return functions[index].name;
}
......
openmmapi/src/CustomHbondForce.cpp
View file @ 75a04e7f
......@@ -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: *
* *
......@@ -193,22 +193,22 @@ void CustomHbondForce::setExclusionParticles(int index, int donor, int acceptor)
exclusions[index].acceptor = acceptor;
}
int CustomHbondForce::addFunction(const std::string& name, TabulatedFunction* function) {
int CustomHbondForce::addTabulatedFunction(const std::string& name, TabulatedFunction* function) {
functions.push_back(FunctionInfo(name, function));
return functions.size()-1;
}
const TabulatedFunction& CustomHbondForce::getFunction(int index) const {
const TabulatedFunction& CustomHbondForce::getTabulatedFunction(int index) const {
ASSERT_VALID_INDEX(index, functions);
return *functions[index].function;
}
TabulatedFunction& CustomHbondForce::getFunction(int index) {
TabulatedFunction& CustomHbondForce::getTabulatedFunction(int index) {
ASSERT_VALID_INDEX(index, functions);
return *functions[index].function;
}
const string& CustomHbondForce::getFunctionName(int index) const {
const string& CustomHbondForce::getTabulatedFunctionName(int index) const {
ASSERT_VALID_INDEX(index, functions);
return functions[index].name;
}
......
openmmapi/src/CustomNonbondedForce.cpp
View file @ 75a04e7f
......@@ -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: *
* *
......@@ -174,22 +174,22 @@ void CustomNonbondedForce::setExclusionParticles(int index, int particle1, int p
exclusions[index].particle1 = particle1;
exclusions[index].particle2 = particle2;
}
int CustomNonbondedForce::addFunction(const std::string& name, TabulatedFunction* function) {
int CustomNonbondedForce::addTabulatedFunction(const std::string& name, TabulatedFunction* function) {
functions.push_back(FunctionInfo(name, function));
return functions.size()-1;
}
const TabulatedFunction& CustomNonbondedForce::getFunction(int index) const {
const TabulatedFunction& CustomNonbondedForce::getTabulatedFunction(int index) const {
ASSERT_VALID_INDEX(index, functions);
return *functions[index].function;
}
TabulatedFunction& CustomNonbondedForce::getFunction(int index) {
TabulatedFunction& CustomNonbondedForce::getTabulatedFunction(int index) {
ASSERT_VALID_INDEX(index, functions);
return *functions[index].function;
}
const string& CustomNonbondedForce::getFunctionName(int index) const {
const string& CustomNonbondedForce::getTabulatedFunctionName(int index) const {
ASSERT_VALID_INDEX(index, functions);
return functions[index].name;
}
......
platforms/cuda/src/CudaExpressionUtilities.cpp
View file @ 75a04e7f
......@@ -468,8 +468,23 @@ string CudaExpressionUtilities::getTempName(const ExpressionTreeNode& node, cons
void CudaExpressionUtilities::findRelatedTabulatedFunctions(const ExpressionTreeNode& node, const ExpressionTreeNode& searchNode,
vector<const Lepton::ExpressionTreeNode*>& nodes) {
if (searchNode.getOperation().getId() == Operation::CUSTOM && node.getChildren()[0] == searchNode.getChildren()[0])
if (searchNode.getOperation().getId() == Operation::CUSTOM && node.getOperation().getName() == searchNode.getOperation().getName()) {
// Make sure the arguments are identical.
for (int i = 0; i < (int) node.getChildren().size(); i++)
if (node.getChildren()[i] != searchNode.getChildren()[i])
return;
// See if we already have an identical node.
for (int i = 0; i < (int) nodes.size(); i++)
if (*nodes[i] == searchNode)
return;
// Add the node.
nodes.push_back(&searchNode);
}
else
for (int i = 0; i < (int) searchNode.getChildren().size(); i++)
findRelatedTabulatedFunctions(node, searchNode.getChildren()[i], nodes);
......
platforms/cuda/src/CudaKernels.cpp
View file @ 75a04e7f
......@@ -1960,13 +1960,13 @@ void CudaCalcCustomNonbondedForceKernel::initialize(const System& system, const
vector<pair<string, string> > functionDefinitions;
vector<const TabulatedFunction*> functionList;
for (int i = 0; i < force.getNumFunctions(); i++) {
functionList.push_back(&force.getFunction(i));
string name = force.getFunctionName(i);
functionList.push_back(&force.getTabulatedFunction(i));
string name = force.getTabulatedFunctionName(i);
string arrayName = prefix+"table"+cu.intToString(i);
functionDefinitions.push_back(make_pair(name, arrayName));
functions[name] = cu.getExpressionUtilities().getFunctionPlaceholder(force.getFunction(i));
functions[name] = cu.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
int width;
vector<float> f = cu.getExpressionUtilities().computeFunctionCoefficients(force.getFunction(i), width);
vector<float> f = cu.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
tabulatedFunctions.push_back(CudaArray::create<float>(cu, f.size(), "TabulatedFunction"));
tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
cu.getNonbondedUtilities().addArgument(CudaNonbondedUtilities::ParameterInfo(arrayName, "float", width, width*sizeof(float), tabulatedFunctions[tabulatedFunctions.size()-1]->getDevicePointer()));
......@@ -2664,18 +2664,21 @@ void CudaCalcCustomGBForceKernel::initialize(const System& system, const CustomG
vector<pair<string, string> > functionDefinitions;
vector<const TabulatedFunction*> functionList;
stringstream tableArgs;
for (int i = 0; i < force.getNumFunctions(); i++) {
functionList.push_back(&force.getFunction(i));
string name = force.getFunctionName(i);
for (int i = 0; i < force.getNumTabulatedFunctions(); i++) {
functionList.push_back(&force.getTabulatedFunction(i));
string name = force.getTabulatedFunctionName(i);
string arrayName = prefix+"table"+cu.intToString(i);
functionDefinitions.push_back(make_pair(name, arrayName));
functions[name] = cu.getExpressionUtilities().getFunctionPlaceholder(force.getFunction(i));
functions[name] = cu.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
int width;
vector<float> f = cu.getExpressionUtilities().computeFunctionCoefficients(force.getFunction(i), width);
vector<float> f = cu.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
tabulatedFunctions.push_back(CudaArray::create<float>(cu, f.size(), "TabulatedFunction"));
tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
cu.getNonbondedUtilities().addArgument(CudaNonbondedUtilities::ParameterInfo(arrayName, "float", width, width*sizeof(float), tabulatedFunctions[tabulatedFunctions.size()-1]->getDevicePointer()));
tableArgs << ", const float4* __restrict__ " << arrayName;
tableArgs << ", const float";
if (width > 1)
tableArgs << width;
tableArgs << "* __restrict__ " << arrayName;
}
// Record the global parameters.
......@@ -3758,13 +3761,13 @@ void CudaCalcCustomHbondForceKernel::initialize(const System& system, const Cust
vector<const TabulatedFunction*> functionList;
stringstream tableArgs;
for (int i = 0; i < force.getNumFunctions(); i++) {
functionList.push_back(&force.getFunction(i));
string name = force.getFunctionName(i);
functionList.push_back(&force.getTabulatedFunction(i));
string name = force.getTabulatedFunctionName(i);
string arrayName = "table"+cu.intToString(i);
functionDefinitions.push_back(make_pair(name, arrayName));
functions[name] = cu.getExpressionUtilities().getFunctionPlaceholder(force.getFunction(i));
functions[name] = cu.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
int width;
vector<float> f = cu.getExpressionUtilities().computeFunctionCoefficients(force.getFunction(i), width);
vector<float> f = cu.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
tabulatedFunctions.push_back(CudaArray::create<float>(cu, f.size(), "TabulatedFunction"));
tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
tableArgs << ", const float";
......@@ -4139,11 +4142,11 @@ void CudaCalcCustomCompoundBondForceKernel::initialize(const System& system, con
vector<const TabulatedFunction*> functionList;
stringstream tableArgs;
for (int i = 0; i < force.getNumFunctions(); i++) {
functionList.push_back(&force.getFunction(i));
string name = force.getFunctionName(i);
functions[name] = cu.getExpressionUtilities().getFunctionPlaceholder(force.getFunction(i));
functionList.push_back(&force.getTabulatedFunction(i));
string name = force.getTabulatedFunctionName(i);
functions[name] = cu.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
int width;
vector<float> f = cu.getExpressionUtilities().computeFunctionCoefficients(force.getFunction(i), width);
vector<float> f = cu.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
CudaArray* array = CudaArray::create<float>(cu, f.size(), "TabulatedFunction");
tabulatedFunctions.push_back(array);
array->upload(f);
......
platforms/cuda/tests/TestCudaCustomCompoundBondForce.cpp
View file @ 75a04e7f
......@@ -220,7 +220,7 @@ void testContinuous2DFunction() {
table[i+xsize*j] = sin(0.25*x)*cos(0.33*y);
}
}
forceField->addFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
forceField->addTabulatedFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(1);
......@@ -270,7 +270,7 @@ void testContinuous3DFunction() {
}
}
}
forceField->addFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
forceField->addTabulatedFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(1);
......
platforms/cuda/tests/TestCudaCustomGBForce.cpp
View file @ 75a04e7f
......@@ -277,7 +277,7 @@ void testTabulatedFunction() {
vector<double> table;
for (int i = 0; i < 21; i++)
table.push_back(std::sin(0.25*i));
force->addFunction("fn", table, 1.0, 6.0);
force->addTabulatedFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
system.addForce(force);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
......
platforms/cuda/tests/TestCudaCustomHbondForce.cpp
View file @ 75a04e7f
......@@ -214,7 +214,7 @@ void testCustomFunctions() {
vector<double> function(2);
function[0] = 0;
function[1] = 1;
custom->addFunction("foo", function, 0, 10);
custom->addTabulatedFunction("foo", new Continuous1DFunction(function, 0, 10));
system.addForce(custom);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
......
platforms/cuda/tests/TestCudaCustomNonbondedForce.cpp
View file @ 75a04e7f
......@@ -272,7 +272,7 @@ void testContinuous1DFunction() {
vector<double> table;
for (int i = 0; i < 21; i++)
table.push_back(sin(0.25*i));
forceField->addFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
forceField->addTabulatedFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
......@@ -322,7 +322,7 @@ void testContinuous2DFunction() {
table[i+xsize*j] = sin(0.25*x)*cos(0.33*y);
}
}
forceField->addFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
forceField->addTabulatedFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
......@@ -377,7 +377,7 @@ void testContinuous3DFunction() {
}
}
}
forceField->addFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
forceField->addTabulatedFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
......@@ -416,7 +416,7 @@ void testDiscrete1DFunction() {
vector<double> table;
for (int i = 0; i < 21; i++)
table.push_back(sin(0.25*i));
forceField->addFunction("fn", new Discrete1DFunction(table));
forceField->addTabulatedFunction("fn", new Discrete1DFunction(table));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
......@@ -447,7 +447,7 @@ void testDiscrete2DFunction() {
for (int i = 0; i < xsize; i++)
for (int j = 0; j < ysize; j++)
table.push_back(sin(0.25*i)+cos(0.33*j));
forceField->addFunction("fn", new Discrete2DFunction(xsize, ysize, table));
forceField->addTabulatedFunction("fn", new Discrete2DFunction(xsize, ysize, table));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
......@@ -482,7 +482,7 @@ void testDiscrete3DFunction() {
for (int j = 0; j < ysize; j++)
for (int k = 0; k < zsize; k++)
table.push_back(sin(0.25*i)+cos(0.33*j)+0.12345*k);
forceField->addFunction("fn", new Discrete3DFunction(xsize, ysize, zsize, table));
forceField->addTabulatedFunction("fn", new Discrete3DFunction(xsize, ysize, zsize, table));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
......
platforms/opencl/src/OpenCLExpressionUtilities.cpp
View file @ 75a04e7f
......@@ -468,8 +468,23 @@ string OpenCLExpressionUtilities::getTempName(const ExpressionTreeNode& node, co
void OpenCLExpressionUtilities::findRelatedTabulatedFunctions(const ExpressionTreeNode& node, const ExpressionTreeNode& searchNode,
vector<const Lepton::ExpressionTreeNode*>& nodes) {
if (searchNode.getOperation().getId() == Operation::CUSTOM && node.getChildren()[0] == searchNode.getChildren()[0])
if (searchNode.getOperation().getId() == Operation::CUSTOM && node.getOperation().getName() == searchNode.getOperation().getName()) {
// Make sure the arguments are identical.
for (int i = 0; i < (int) node.getChildren().size(); i++)
if (node.getChildren()[i] != searchNode.getChildren()[i])
return;
// See if we already have an identical node.
for (int i = 0; i < (int) nodes.size(); i++)
if (*nodes[i] == searchNode)
return;
// Add the node.
nodes.push_back(&searchNode);
}
else
for (int i = 0; i < (int) searchNode.getChildren().size(); i++)
findRelatedTabulatedFunctions(node, searchNode.getChildren()[i], nodes);
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ 75a04e7f
......@@ -1970,13 +1970,13 @@ void OpenCLCalcCustomNonbondedForceKernel::initialize(const System& system, cons
vector<pair<string, string> > functionDefinitions;
vector<const TabulatedFunction*> functionList;
for (int i = 0; i < force.getNumFunctions(); i++) {
functionList.push_back(&force.getFunction(i));
string name = force.getFunctionName(i);
functionList.push_back(&force.getTabulatedFunction(i));
string name = force.getTabulatedFunctionName(i);
string arrayName = prefix+"table"+cl.intToString(i);
functionDefinitions.push_back(make_pair(name, arrayName));
functions[name] = cl.getExpressionUtilities().getFunctionPlaceholder(force.getFunction(i));
functions[name] = cl.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
int width;
vector<float> f = cl.getExpressionUtilities().computeFunctionCoefficients(force.getFunction(i), width);
vector<float> f = cl.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
tabulatedFunctions.push_back(OpenCLArray::create<float>(cl, f.size(), "TabulatedFunction"));
tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
cl.getNonbondedUtilities().addArgument(OpenCLNonbondedUtilities::ParameterInfo(arrayName, "float", width, width*sizeof(float), tabulatedFunctions[tabulatedFunctions.size()-1]->getDeviceBuffer()));
......@@ -2717,18 +2717,21 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
vector<pair<string, string> > functionDefinitions;
vector<const TabulatedFunction*> functionList;
stringstream tableArgs;
for (int i = 0; i < force.getNumFunctions(); i++) {
functionList.push_back(&force.getFunction(i));
string name = force.getFunctionName(i);
for (int i = 0; i < force.getNumTabulatedFunctions(); i++) {
functionList.push_back(&force.getTabulatedFunction(i));
string name = force.getTabulatedFunctionName(i);
string arrayName = prefix+"table"+cl.intToString(i);
functionDefinitions.push_back(make_pair(name, arrayName));
functions[name] = cl.getExpressionUtilities().getFunctionPlaceholder(force.getFunction(i));
functions[name] = cl.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
int width;
vector<float> f = cl.getExpressionUtilities().computeFunctionCoefficients(force.getFunction(i), width);
vector<float> f = cl.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
tabulatedFunctions.push_back(OpenCLArray::create<float>(cl, f.size(), "TabulatedFunction"));
tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
cl.getNonbondedUtilities().addArgument(OpenCLNonbondedUtilities::ParameterInfo(arrayName, "float", width, width*sizeof(float), tabulatedFunctions[tabulatedFunctions.size()-1]->getDeviceBuffer()));
tableArgs << ", __global const float4* restrict " << arrayName;
tableArgs << ", __global const float";
if (width > 1)
tableArgs << width;
tableArgs << "* restrict " << arrayName;
}
// Record the global parameters.
......@@ -3921,13 +3924,13 @@ void OpenCLCalcCustomHbondForceKernel::initialize(const System& system, const Cu
vector<const TabulatedFunction*> functionList;
stringstream tableArgs;
for (int i = 0; i < force.getNumFunctions(); i++) {
functionList.push_back(&force.getFunction(i));
string name = force.getFunctionName(i);
functionList.push_back(&force.getTabulatedFunction(i));
string name = force.getTabulatedFunctionName(i);
string arrayName = "table"+cl.intToString(i);
functionDefinitions.push_back(make_pair(name, arrayName));
functions[name] = cl.getExpressionUtilities().getFunctionPlaceholder(force.getFunction(i));
functions[name] = cl.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
int width;
vector<float> f = cl.getExpressionUtilities().computeFunctionCoefficients(force.getFunction(i), width);
vector<float> f = cl.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
tabulatedFunctions.push_back(OpenCLArray::create<float>(cl, f.size(), "TabulatedFunction"));
tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
tableArgs << ", __global const float";
......@@ -4304,11 +4307,11 @@ void OpenCLCalcCustomCompoundBondForceKernel::initialize(const System& system, c
vector<const TabulatedFunction*> functionList;
stringstream tableArgs;
for (int i = 0; i < force.getNumFunctions(); i++) {
functionList.push_back(&force.getFunction(i));
string name = force.getFunctionName(i);
functions[name] = cl.getExpressionUtilities().getFunctionPlaceholder(force.getFunction(i));
functionList.push_back(&force.getTabulatedFunction(i));
string name = force.getTabulatedFunctionName(i);
functions[name] = cl.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
int width;
vector<float> f = cl.getExpressionUtilities().computeFunctionCoefficients(force.getFunction(i), width);
vector<float> f = cl.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
OpenCLArray* array = OpenCLArray::create<float>(cl, f.size(), "TabulatedFunction");
tabulatedFunctions.push_back(array);
array->upload(f);
......
platforms/opencl/tests/TestOpenCLCustomCompoundBondForce.cpp
View file @ 75a04e7f
......@@ -220,7 +220,7 @@ void testContinuous2DFunction() {
table[i+xsize*j] = sin(0.25*x)*cos(0.33*y);
}
}
forceField->addFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
forceField->addTabulatedFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(1);
......@@ -270,7 +270,7 @@ void testContinuous3DFunction() {
}
}
}
forceField->addFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
forceField->addTabulatedFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(1);
......
platforms/opencl/tests/TestOpenCLCustomGBForce.cpp
View file @ 75a04e7f
......@@ -277,7 +277,7 @@ void testTabulatedFunction() {
vector<double> table;
for (int i = 0; i < 21; i++)
table.push_back(std::sin(0.25*i));
force->addFunction("fn", table, 1.0, 6.0);
force->addTabulatedFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
system.addForce(force);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
......
platforms/opencl/tests/TestOpenCLCustomHbondForce.cpp
View file @ 75a04e7f
......@@ -214,7 +214,7 @@ void testCustomFunctions() {
vector<double> function(2);
function[0] = 0;
function[1] = 1;
custom->addFunction("foo", function, 0, 10);
custom->addTabulatedFunction("foo", new Continuous1DFunction(function, 0, 10));
system.addForce(custom);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
......
platforms/opencl/tests/TestOpenCLCustomNonbondedForce.cpp
View file @ 75a04e7f
......@@ -272,7 +272,7 @@ void testContinuous1DFunction() {
vector<double> table;
for (int i = 0; i < 21; i++)
table.push_back(sin(0.25*i));
forceField->addFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
forceField->addTabulatedFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
......@@ -322,7 +322,7 @@ void testContinuous2DFunction() {
table[i+xsize*j] = sin(0.25*x)*cos(0.33*y);
}
}
forceField->addFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
forceField->addTabulatedFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
......@@ -377,7 +377,7 @@ void testContinuous3DFunction() {
}
}
}
forceField->addFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
forceField->addTabulatedFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
......@@ -416,7 +416,7 @@ void testDiscrete1DFunction() {
vector<double> table;
for (int i = 0; i < 21; i++)
table.push_back(sin(0.25*i));
forceField->addFunction("fn", new Discrete1DFunction(table));
forceField->addTabulatedFunction("fn", new Discrete1DFunction(table));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
......@@ -446,7 +446,7 @@ void testDiscrete2DFunction() {
for (int i = 0; i < xsize; i++)
for (int j = 0; j < ysize; j++)
table.push_back(sin(0.25*i)+cos(0.33*j));
forceField->addFunction("fn", new Discrete2DFunction(xsize, ysize, table));
forceField->addTabulatedFunction("fn", new Discrete2DFunction(xsize, ysize, table));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
......@@ -481,7 +481,7 @@ void testDiscrete3DFunction() {
for (int j = 0; j < ysize; j++)
for (int k = 0; k < zsize; k++)
table.push_back(sin(0.25*i)+cos(0.33*j)+0.12345*k);
forceField->addFunction("fn", new Discrete3DFunction(xsize, ysize, zsize, table));
forceField->addTabulatedFunction("fn", new Discrete3DFunction(xsize, ysize, zsize, table));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
......
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