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Commit 2e9c418a authored by peastman's avatar peastman
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Merge branch 'master' into gayberne

parents 8f532e31 a4d327f5
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olla/src/Platform.cpp
View file @ 2e9c418a
......@@ -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) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -89,15 +89,21 @@ void Platform::setPropertyValue(Context& context, const string& property, const
}
const string& Platform::getPropertyDefaultValue(const string& property) const {
map<string, string>::const_iterator value = defaultProperties.find(property);
string propertyName = property;
if (deprecatedPropertyReplacements.find(property) != deprecatedPropertyReplacements.end())
propertyName = deprecatedPropertyReplacements.find(property)->second;
map<string, string>::const_iterator value = defaultProperties.find(propertyName);
if (value == defaultProperties.end())
throw OpenMMException("getPropertyDefaultValue: Illegal property name");
return value->second;
}
void Platform::setPropertyDefaultValue(const string& property, const string& value) {
string propertyName = property;
if (deprecatedPropertyReplacements.find(property) != deprecatedPropertyReplacements.end())
propertyName = deprecatedPropertyReplacements.find(property)->second;
for (int i = 0; i < (int) platformProperties.size(); i++)
if (platformProperties[i] == property) {
if (platformProperties[i] == propertyName) {
defaultProperties[property] = value;
return;
}
......
openmmapi/include/openmm/CMAPTorsionForce.h
View file @ 2e9c418a
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010-2015 Stanford University and the Authors. *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -159,15 +159,18 @@ public:
* new bonds and torsions cannot be added.
*/
void updateParametersInContext(Context& context);
/**
* Set whether this force should apply periodic boundary conditions when calculating displacements.
* Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
*/
void setUsesPeriodicBoundaryConditions(bool periodic);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns false
* @returns true if force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return false;
}
bool usesPeriodicBoundaryConditions() const;
protected:
ForceImpl* createImpl() const;
private:
......@@ -175,6 +178,7 @@ private:
class CMAPTorsionInfo;
std::vector<MapInfo> maps;
std::vector<CMAPTorsionInfo> torsions;
bool usePeriodic;
};
/**
......
openmmapi/include/openmm/CustomAngleForce.h
View file @ 2e9c418a
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010-2012 Stanford University and the Authors. *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -203,15 +203,18 @@ public:
* the Context. The set of particles involved in a angle cannot be changed, nor can new angles be added.
*/
void updateParametersInContext(Context& context);
/**
* Set whether this force should apply periodic boundary conditions when calculating displacements.
* Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
*/
void setUsesPeriodicBoundaryConditions(bool periodic);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns false
* @returns true if force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return false;
}
bool usesPeriodicBoundaryConditions() const;
protected:
ForceImpl* createImpl() const;
private:
......@@ -222,6 +225,7 @@ private:
std::vector<AngleParameterInfo> parameters;
std::vector<GlobalParameterInfo> globalParameters;
std::vector<AngleInfo> angles;
bool usePeriodic;
};
/**
......
openmmapi/include/openmm/CustomBondForce.h
View file @ 2e9c418a
......@@ -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) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -200,15 +200,18 @@ public:
* the Context. The set of particles involved in a bond cannot be changed, nor can new bonds be added.
*/
void updateParametersInContext(Context& context);
/**
* Set whether this force should apply periodic boundary conditions when calculating displacements.
* Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
*/
void setUsesPeriodicBoundaryConditions(bool periodic);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns false
* @returns true if force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return false;
}
bool usesPeriodicBoundaryConditions() const;
protected:
ForceImpl* createImpl() const;
private:
......@@ -219,6 +222,7 @@ private:
std::vector<BondParameterInfo> parameters;
std::vector<GlobalParameterInfo> globalParameters;
std::vector<BondInfo> bonds;
bool usePeriodic;
};
/**
......
openmmapi/include/openmm/CustomCentroidBondForce.h
View file @ 2e9c418a
......@@ -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) 2008-2015 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -324,15 +324,18 @@ public:
* bonds be added.
*/
void updateParametersInContext(Context& context);
/**
* Set whether this force should apply periodic boundary conditions when calculating displacements.
* Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
*/
void setUsesPeriodicBoundaryConditions(bool periodic);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns false
* @returns true if force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return false;
}
bool usesPeriodicBoundaryConditions() const;
protected:
ForceImpl* createImpl() const;
private:
......@@ -348,6 +351,7 @@ private:
std::vector<GroupInfo> groups;
std::vector<BondInfo> bonds;
std::vector<FunctionInfo> functions;
bool usePeriodic;
};
/**
......
openmmapi/include/openmm/CustomCompoundBondForce.h
View file @ 2e9c418a
......@@ -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) 2008-2014 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -298,15 +298,18 @@ public:
* the Context. The set of particles involved in a bond cannot be changed, nor can new bonds be added.
*/
void updateParametersInContext(Context& context);
/**
* Set whether this force should apply periodic boundary conditions when calculating displacements.
* Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
*/
void setUsesPeriodicBoundaryConditions(bool periodic);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns false
* @returns true if force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return false;
}
bool usesPeriodicBoundaryConditions() const;
protected:
ForceImpl* createImpl() const;
private:
......@@ -320,6 +323,7 @@ private:
std::vector<GlobalParameterInfo> globalParameters;
std::vector<BondInfo> bonds;
std::vector<FunctionInfo> functions;
bool usePeriodic;
};
/**
......
openmmapi/include/openmm/CustomIntegrator.h
View file @ 2e9c418a
......@@ -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) 2011-2012 Stanford University and the Authors. *
* Portions copyright (c) 2011-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -266,15 +266,15 @@ public:
/**
* Begin an "if" block.
*/
BeginIfBlock = 6,
IfBlockStart = 6,
/**
* Begin a while" block.
*/
BeginWhileBlock = 7,
WhileBlockStart = 7,
/**
* End an "if" or "while" block.
*/
EndBlock = 8
BlockEnd = 8
};
/**
* Create a CustomIntegrator.
......
openmmapi/include/openmm/CustomTorsionForce.h
View file @ 2e9c418a
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010-2012 Stanford University and the Authors. *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -206,15 +206,18 @@ public:
* the Context. The set of particles involved in a torsion cannot be changed, nor can new torsions be added.
*/
void updateParametersInContext(Context& context);
/**
* Set whether this force should apply periodic boundary conditions when calculating displacements.
* Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
*/
void setUsesPeriodicBoundaryConditions(bool periodic);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns true if force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return false;
}
bool usesPeriodicBoundaryConditions() const;
protected:
ForceImpl* createImpl() const;
private:
......@@ -225,6 +228,7 @@ private:
std::vector<TorsionParameterInfo> parameters;
std::vector<GlobalParameterInfo> globalParameters;
std::vector<TorsionInfo> torsions;
bool usePeriodic;
};
/**
......
openmmapi/include/openmm/HarmonicAngleForce.h
View file @ 2e9c418a
......@@ -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) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -102,20 +102,23 @@ public:
* in a angle cannot be changed, nor can new angles be added.
*/
void updateParametersInContext(Context& context);
/**
* Set whether this force should apply periodic boundary conditions when calculating displacements.
* Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
*/
void setUsesPeriodicBoundaryConditions(bool periodic);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns true if force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return false;
}
protected:
bool usesPeriodicBoundaryConditions() const;protected:
ForceImpl* createImpl() const;
private:
class AngleInfo;
std::vector<AngleInfo> angles;
bool usePeriodic;
};
/**
......
openmmapi/include/openmm/HarmonicBondForce.h
View file @ 2e9c418a
......@@ -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) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -99,20 +99,24 @@ public:
* in a bond cannot be changed, nor can new bonds be added.
*/
void updateParametersInContext(Context& context);
/**
* Set whether this force should apply periodic boundary conditions when calculating displacements.
* Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
*/
void setUsesPeriodicBoundaryConditions(bool periodic);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns true if force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return false;
}
bool usesPeriodicBoundaryConditions() const;
protected:
ForceImpl* createImpl() const;
private:
class BondInfo;
std::vector<BondInfo> bonds;
bool usePeriodic;
};
/**
......
openmmapi/include/openmm/MonteCarloAnisotropicBarostat.h
View file @ 2e9c418a
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010-2013 Stanford University and the Authors. *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman, Lee-Ping Wang *
* Contributors: *
* *
......@@ -81,17 +81,25 @@ public:
static const std::string key = "MonteCarloPressureZ";
return key;
}
/**
* This is the name of the parameter which stores the current temperature at which the
* system is being maintained (in Kelvin)
*/
static const std::string& Temperature() {
static const std::string key = "AnisotropicMonteCarloTemperature";
return key;
}
/**
* Create a MonteCarloAnisotropicBarostat.
*
* @param defaultPressure The default pressure acting on each axis (in bar)
* @param temperature the temperature at which the system is being maintained (in Kelvin)
* @param scaleX whether to allow the X dimension of the periodic box to change size
* @param scaleY whether to allow the Y dimension of the periodic box to change size
* @param scaleZ whether to allow the Z dimension of the periodic box to change size
* @param frequency the frequency at which Monte Carlo pressure changes should be attempted (in time steps)
* @param defaultPressure The default pressure acting on each axis (in bar)
* @param defaultTemperature the default temperature at which the system is being maintained (in Kelvin)
* @param scaleX whether to allow the X dimension of the periodic box to change size
* @param scaleY whether to allow the Y dimension of the periodic box to change size
* @param scaleZ whether to allow the Z dimension of the periodic box to change size
* @param frequency the frequency at which Monte Carlo pressure changes should be attempted (in time steps)
*/
MonteCarloAnisotropicBarostat(const Vec3& defaultPressure, double temperature, bool scaleX = true, bool scaleY = true, bool scaleZ = true, int frequency = 25);
MonteCarloAnisotropicBarostat(const Vec3& defaultPressure, double defaultTemperature, bool scaleX = true, bool scaleY = true, bool scaleZ = true, int frequency = 25);
/**
* Get the default pressure (in bar).
*
......@@ -142,18 +150,19 @@ public:
frequency = freq;
}
/**
* Get the temperature at which the system is being maintained, measured in Kelvin.
* Get the default temperature at which the system is being maintained, measured in Kelvin.
*/
double getTemperature() const {
return temperature;
double getDefaultTemperature() const {
return defaultTemperature;
}
/**
* Set the temperature at which the system is being maintained.
* Set the default temperature at which the system is being maintained. This will affect any new Contexts you create,
* but not ones that already exist.
*
* @param temp the system temperature, measured in Kelvin.
*/
void setTemperature(double temp) {
temperature = temp;
void setDefaultTemperature(double temp) {
defaultTemperature = temp;
}
/**
* Get the random number seed. See setRandomNumberSeed() for details.
......@@ -188,7 +197,7 @@ protected:
ForceImpl* createImpl() const;
private:
Vec3 defaultPressure;
double temperature;
double defaultTemperature;
bool scaleX, scaleY, scaleZ;
int frequency, randomNumberSeed;
};
......
openmmapi/include/openmm/MonteCarloBarostat.h
View file @ 2e9c418a
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -58,14 +58,22 @@ public:
static const std::string key = "MonteCarloPressure";
return key;
}
/**
* This is the name of the parameter which stores the current temperature at which the
* system is being maintained (in Kelvin)
*/
static const std::string& Temperature() {
static const std::string key = "MonteCarloTemperature";
return key;
}
/**
* Create a MonteCarloBarostat.
*
* @param defaultPressure the default pressure acting on the system (in bar)
* @param temperature the temperature at which the system is being maintained (in Kelvin)
* @param frequency the frequency at which Monte Carlo pressure changes should be attempted (in time steps)
* @param defaultPressure the default pressure acting on the system (in bar)
* @param defaultTemperature the default temperature at which the system is being maintained (in Kelvin)
* @param frequency the frequency at which Monte Carlo pressure changes should be attempted (in time steps)
*/
MonteCarloBarostat(double defaultPressure, double temperature, int frequency = 25);
MonteCarloBarostat(double defaultPressure, double defaultTemperature, int frequency = 25);
/**
* Get the default pressure acting on the system (in bar).
*
......@@ -98,18 +106,19 @@ public:
frequency = freq;
}
/**
* Get the temperature at which the system is being maintained, measured in Kelvin.
* Get the default temperature at which the system is being maintained, measured in Kelvin.
*/
double getTemperature() const {
return temperature;
double getDefaultTemperature() const {
return defaultTemperature;
}
/**
* Set the temperature at which the system is being maintained.
* Set the default temperature at which the system is being maintained. This will affect any new Contexts you create,
* but not ones that already exist.
*
* @param temp the system temperature, measured in Kelvin.
*/
void setTemperature(double temp) {
temperature = temp;
void setDefaultTemperature(double temp) {
defaultTemperature = temp;
}
/**
* Get the random number seed. See setRandomNumberSeed() for details.
......@@ -143,7 +152,7 @@ public:
protected:
ForceImpl* createImpl() const;
private:
double defaultPressure, temperature;
double defaultPressure, defaultTemperature;
int frequency, randomNumberSeed;
};
......
openmmapi/include/openmm/MonteCarloMembraneBarostat.h
View file @ 2e9c418a
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -111,17 +111,25 @@ public:
static const std::string key = "MembraneMonteCarloSurfaceTension";
return key;
}
/**
* This is the name of the parameter which stores the current temperature at which the
* system is being maintained (in Kelvin)
*/
static const std::string& Temperature() {
static const std::string key = "MembraneMonteCarloTemperature";
return key;
}
/**
* Create a MonteCarloMembraneBarostat.
*
* @param defaultPressure the default pressure acting on the system (in bar)
* @param defaultSurfaceTension the default surface tension acting on the system (in bar*nm)
* @param temperature the temperature at which the system is being maintained (in Kelvin)
* @param defaultTemperature the default temperature at which the system is being maintained (in Kelvin)
* @param xymode the mode specifying the behavior of the X and Y axes
* @param zmode the mode specifying the behavior of the Z axis
* @param frequency the frequency at which Monte Carlo volume changes should be attempted (in time steps)
*/
MonteCarloMembraneBarostat(double defaultPressure, double defaultSurfaceTension, double temperature, XYMode xymode, ZMode zmode, int frequency = 25);
MonteCarloMembraneBarostat(double defaultPressure, double defaultSurfaceTension, double defaultTemperature, XYMode xymode, ZMode zmode, int frequency = 25);
/**
* Get the default pressure acting on the system (in bar).
*
......@@ -171,18 +179,19 @@ public:
frequency = freq;
}
/**
* Get the temperature at which the system is being maintained, measured in Kelvin.
* Get the default temperature at which the system is being maintained, measured in Kelvin.
*/
double getTemperature() const {
return temperature;
double getDefaultTemperature() const {
return defaultTemperature;
}
/**
* Set the temperature at which the system is being maintained.
* Set the default temperature at which the system is being maintained. This will affect any new Contexts you create,
* but not ones that already exist.
*
* @param temp the system temperature, measured in Kelvin.
*/
void setTemperature(double temp) {
temperature = temp;
void setDefaultTemperature(double temp) {
defaultTemperature = temp;
}
/**
* Get the mode specifying the behavior of the X and Y axes.
......@@ -240,7 +249,7 @@ public:
protected:
ForceImpl* createImpl() const;
private:
double defaultPressure, defaultSurfaceTension, temperature;
double defaultPressure, defaultSurfaceTension, defaultTemperature;
XYMode xymode;
ZMode zmode;
int frequency, randomNumberSeed;
......
openmmapi/include/openmm/PeriodicTorsionForce.h
View file @ 2e9c418a
......@@ -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) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -108,20 +108,24 @@ public:
* in a torsion cannot be changed, nor can new torsions be added.
*/
void updateParametersInContext(Context& context);
/**
* Set whether this force should apply periodic boundary conditions when calculating displacements.
* Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
*/
void setUsesPeriodicBoundaryConditions(bool periodic);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns true if force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return false;
}
bool usesPeriodicBoundaryConditions() const;
protected:
ForceImpl* createImpl() const;
private:
class PeriodicTorsionInfo;
std::vector<PeriodicTorsionInfo> periodicTorsions;
bool usePeriodic;
};
/**
......
openmmapi/include/openmm/RBTorsionForce.h
View file @ 2e9c418a
......@@ -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) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -117,20 +117,24 @@ public:
* in a torsion cannot be changed, nor can new torsions be added.
*/
void updateParametersInContext(Context& context);
/**
* Set whether this force should apply periodic boundary conditions when calculating displacements.
* Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
*/
void setUsesPeriodicBoundaryConditions(bool periodic);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns true if force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return false;
}
bool usesPeriodicBoundaryConditions() const;
protected:
ForceImpl* createImpl() const;
private:
class RBTorsionInfo;
std::vector<RBTorsionInfo> rbTorsions;
bool usePeriodic;
};
/**
......
openmmapi/include/openmm/internal/OSRngSeed.h
View file @ 2e9c418a
#ifndef OPENMM_OSRNGSEED_H_
#ifndef OPENMM_OSRNGSEED_H_
#define OPENMM_OSRNGSEED_H_
......
openmmapi/src/CMAPTorsionForce.cpp
View file @ 2e9c418a
......@@ -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) 2010-2015 Stanford University and the Authors. *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -37,7 +37,7 @@
using namespace OpenMM;
CMAPTorsionForce::CMAPTorsionForce() {
CMAPTorsionForce::CMAPTorsionForce() : usePeriodic(false) {
}
int CMAPTorsionForce::addMap(int size, const std::vector<double>& energy) {
......@@ -99,3 +99,11 @@ ForceImpl* CMAPTorsionForce::createImpl() const {
void CMAPTorsionForce::updateParametersInContext(Context& context) {
dynamic_cast<CMAPTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void CMAPTorsionForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool CMAPTorsionForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
openmmapi/src/ContextImpl.cpp
View file @ 2e9c418a
......@@ -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) 2008-2013 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -84,15 +84,20 @@ ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integ
// Validate the list of properties.
const vector<string>& platformProperties = platform->getPropertyNames();
map<string, string> validatedProperties;
for (map<string, string>::const_iterator iter = properties.begin(); iter != properties.end(); ++iter) {
string property = iter->first;
if (platform->deprecatedPropertyReplacements.find(property) != platform->deprecatedPropertyReplacements.end())
property = platform->deprecatedPropertyReplacements[property];
bool valid = false;
for (int i = 0; i < (int) platformProperties.size(); i++)
if (platformProperties[i] == iter->first) {
if (platformProperties[i] == property) {
valid = true;
break;
}
if (!valid)
throw OpenMMException("Illegal property name: "+iter->first);
validatedProperties[property] = iter->second;
}
// Find the list of kernels required.
......@@ -139,7 +144,7 @@ ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integ
for (int i = candidatePlatforms.size()-1; i >= 0; i--) {
try {
this->platform = platform = candidatePlatforms[i].second;
platform->contextCreated(*this, properties);
platform->contextCreated(*this, validatedProperties);
break;
}
catch (...) {
......
openmmapi/src/CustomAngleForce.cpp
View file @ 2e9c418a
......@@ -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) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -44,7 +44,7 @@ using std::string;
using std::stringstream;
using std::vector;
CustomAngleForce::CustomAngleForce(const string& energy) : energyExpression(energy) {
CustomAngleForce::CustomAngleForce(const string& energy) : energyExpression(energy), usePeriodic(false) {
}
const string& CustomAngleForce::getEnergyFunction() const {
......@@ -123,3 +123,11 @@ ForceImpl* CustomAngleForce::createImpl() const {
void CustomAngleForce::updateParametersInContext(Context& context) {
dynamic_cast<CustomAngleForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void CustomAngleForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool CustomAngleForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
openmmapi/src/CustomBondForce.cpp
View file @ 2e9c418a
......@@ -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) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -44,7 +44,7 @@ using std::string;
using std::stringstream;
using std::vector;
CustomBondForce::CustomBondForce(const string& energy) : energyExpression(energy) {
CustomBondForce::CustomBondForce(const string& energy) : energyExpression(energy), usePeriodic(false) {
}
const string& CustomBondForce::getEnergyFunction() const {
......@@ -121,3 +121,11 @@ ForceImpl* CustomBondForce::createImpl() const {
void CustomBondForce::updateParametersInContext(Context& context) {
dynamic_cast<CustomBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void CustomBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool CustomBondForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
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