Skip to content

GitLab

Commit 73183c61 authored by ChayaSt's avatar ChayaSt
Browse files

resolved conflict

parents 0e218233 32e08b87
Show whitespace changes
Inline Side-by-side
Showing with 204 additions and 86 deletions
openmmapi/include/openmm/HarmonicAngleForce.h
View file @ 73183c61
...@@ -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) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -102,20 +102,23 @@ public: ...@@ -102,20 +102,23 @@ public:
* in a angle cannot be changed, nor can new angles be added. * in a angle cannot be changed, nor can new angles be added.
*/ */
void updateParametersInContext(Context& context); 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 * Returns whether or not this force makes use of periodic boundary
* conditions. * conditions.
* *
* @returns true if force uses PBC and false otherwise * @returns true if force uses PBC and false otherwise
*/ */
bool usesPeriodicBoundaryConditions() const { bool usesPeriodicBoundaryConditions() const;protected:
return false;
}
protected:
ForceImpl* createImpl() const; ForceImpl* createImpl() const;
private: private:
class AngleInfo; class AngleInfo;
std::vector<AngleInfo> angles; std::vector<AngleInfo> angles;
bool usePeriodic;
}; };
/** /**
......
openmmapi/include/openmm/HarmonicBondForce.h
View file @ 73183c61
...@@ -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) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -99,20 +99,24 @@ public: ...@@ -99,20 +99,24 @@ public:
* in a bond cannot be changed, nor can new bonds be added. * in a bond cannot be changed, nor can new bonds be added.
*/ */
void updateParametersInContext(Context& context); 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 * Returns whether or not this force makes use of periodic boundary
* conditions. * conditions.
* *
* @returns true if force uses PBC and false otherwise * @returns true if force uses PBC and false otherwise
*/ */
bool usesPeriodicBoundaryConditions() const { bool usesPeriodicBoundaryConditions() const;
return false;
}
protected: protected:
ForceImpl* createImpl() const; ForceImpl* createImpl() const;
private: private:
class BondInfo; class BondInfo;
std::vector<BondInfo> bonds; std::vector<BondInfo> bonds;
bool usePeriodic;
}; };
/** /**
......
openmmapi/include/openmm/MonteCarloAnisotropicBarostat.h
View file @ 73183c61
...@@ -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) 2010-2013 Stanford University and the Authors. * * Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman, Lee-Ping Wang * * Authors: Peter Eastman, Lee-Ping Wang *
* Contributors: * * Contributors: *
* * * *
...@@ -81,17 +81,25 @@ public: ...@@ -81,17 +81,25 @@ public:
static const std::string key = "MonteCarloPressureZ"; static const std::string key = "MonteCarloPressureZ";
return key; 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. * Create a MonteCarloAnisotropicBarostat.
* *
* @param defaultPressure The default pressure acting on each axis (in bar) * @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 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 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 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 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 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). * Get the default pressure (in bar).
* *
...@@ -142,18 +150,19 @@ public: ...@@ -142,18 +150,19 @@ public:
frequency = freq; 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 { double getDefaultTemperature() const {
return temperature; 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. * @param temp the system temperature, measured in Kelvin.
*/ */
void setTemperature(double temp) { void setDefaultTemperature(double temp) {
temperature = temp; defaultTemperature = temp;
} }
/** /**
* Get the random number seed. See setRandomNumberSeed() for details. * Get the random number seed. See setRandomNumberSeed() for details.
...@@ -188,7 +197,7 @@ protected: ...@@ -188,7 +197,7 @@ protected:
ForceImpl* createImpl() const; ForceImpl* createImpl() const;
private: private:
Vec3 defaultPressure; Vec3 defaultPressure;
double temperature; double defaultTemperature;
bool scaleX, scaleY, scaleZ; bool scaleX, scaleY, scaleZ;
int frequency, randomNumberSeed; int frequency, randomNumberSeed;
}; };
......
openmmapi/include/openmm/MonteCarloBarostat.h
View file @ 73183c61
...@@ -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) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -58,14 +58,22 @@ public: ...@@ -58,14 +58,22 @@ public:
static const std::string key = "MonteCarloPressure"; static const std::string key = "MonteCarloPressure";
return key; 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. * Create a MonteCarloBarostat.
* *
* @param defaultPressure the default pressure acting on the system (in bar) * @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 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) * @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). * Get the default pressure acting on the system (in bar).
* *
...@@ -98,18 +106,19 @@ public: ...@@ -98,18 +106,19 @@ public:
frequency = freq; 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 { double getDefaultTemperature() const {
return temperature; 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. * @param temp the system temperature, measured in Kelvin.
*/ */
void setTemperature(double temp) { void setDefaultTemperature(double temp) {
temperature = temp; defaultTemperature = temp;
} }
/** /**
* Get the random number seed. See setRandomNumberSeed() for details. * Get the random number seed. See setRandomNumberSeed() for details.
...@@ -143,7 +152,7 @@ public: ...@@ -143,7 +152,7 @@ public:
protected: protected:
ForceImpl* createImpl() const; ForceImpl* createImpl() const;
private: private:
double defaultPressure, temperature; double defaultPressure, defaultTemperature;
int frequency, randomNumberSeed; int frequency, randomNumberSeed;
}; };
......
openmmapi/include/openmm/MonteCarloMembraneBarostat.h
View file @ 73183c61
...@@ -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) 2010-2014 Stanford University and the Authors. * * Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -111,17 +111,25 @@ public: ...@@ -111,17 +111,25 @@ public:
static const std::string key = "MembraneMonteCarloSurfaceTension"; static const std::string key = "MembraneMonteCarloSurfaceTension";
return key; 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. * Create a MonteCarloMembraneBarostat.
* *
* @param defaultPressure the default pressure acting on the system (in bar) * @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 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 xymode the mode specifying the behavior of the X and Y axes
* @param zmode the mode specifying the behavior of the Z axis * @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) * @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). * Get the default pressure acting on the system (in bar).
* *
...@@ -171,18 +179,19 @@ public: ...@@ -171,18 +179,19 @@ public:
frequency = freq; 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 { double getDefaultTemperature() const {
return temperature; 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. * @param temp the system temperature, measured in Kelvin.
*/ */
void setTemperature(double temp) { void setDefaultTemperature(double temp) {
temperature = temp; defaultTemperature = temp;
} }
/** /**
* Get the mode specifying the behavior of the X and Y axes. * Get the mode specifying the behavior of the X and Y axes.
...@@ -240,7 +249,7 @@ public: ...@@ -240,7 +249,7 @@ public:
protected: protected:
ForceImpl* createImpl() const; ForceImpl* createImpl() const;
private: private:
double defaultPressure, defaultSurfaceTension, temperature; double defaultPressure, defaultSurfaceTension, defaultTemperature;
XYMode xymode; XYMode xymode;
ZMode zmode; ZMode zmode;
int frequency, randomNumberSeed; int frequency, randomNumberSeed;
......
openmmapi/include/openmm/PeriodicTorsionForce.h
View file @ 73183c61
...@@ -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) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -108,20 +108,24 @@ public: ...@@ -108,20 +108,24 @@ public:
* in a torsion cannot be changed, nor can new torsions be added. * in a torsion cannot be changed, nor can new torsions be added.
*/ */
void updateParametersInContext(Context& context); 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 * Returns whether or not this force makes use of periodic boundary
* conditions. * conditions.
* *
* @returns true if force uses PBC and false otherwise * @returns true if force uses PBC and false otherwise
*/ */
bool usesPeriodicBoundaryConditions() const { bool usesPeriodicBoundaryConditions() const;
return false;
}
protected: protected:
ForceImpl* createImpl() const; ForceImpl* createImpl() const;
private: private:
class PeriodicTorsionInfo; class PeriodicTorsionInfo;
std::vector<PeriodicTorsionInfo> periodicTorsions; std::vector<PeriodicTorsionInfo> periodicTorsions;
bool usePeriodic;
}; };
/** /**
......
openmmapi/include/openmm/RBTorsionForce.h
View file @ 73183c61
...@@ -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) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -117,20 +117,24 @@ public: ...@@ -117,20 +117,24 @@ public:
* in a torsion cannot be changed, nor can new torsions be added. * in a torsion cannot be changed, nor can new torsions be added.
*/ */
void updateParametersInContext(Context& context); 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 * Returns whether or not this force makes use of periodic boundary
* conditions. * conditions.
* *
* @returns true if force uses PBC and false otherwise * @returns true if force uses PBC and false otherwise
*/ */
bool usesPeriodicBoundaryConditions() const { bool usesPeriodicBoundaryConditions() const;
return false;
}
protected: protected:
ForceImpl* createImpl() const; ForceImpl* createImpl() const;
private: private:
class RBTorsionInfo; class RBTorsionInfo;
std::vector<RBTorsionInfo> rbTorsions; std::vector<RBTorsionInfo> rbTorsions;
bool usePeriodic;
}; };
/** /**
......
openmmapi/include/openmm/internal/OSRngSeed.h
View file @ 73183c61
#ifndef OPENMM_OSRNGSEED_H_ #ifndef OPENMM_OSRNGSEED_H_
#define OPENMM_OSRNGSEED_H_ #define OPENMM_OSRNGSEED_H_
......
openmmapi/src/CMAPTorsionForce.cpp
View file @ 73183c61
...@@ -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) 2010-2015 Stanford University and the Authors. * * Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -37,7 +37,7 @@ ...@@ -37,7 +37,7 @@
using namespace OpenMM; using namespace OpenMM;
CMAPTorsionForce::CMAPTorsionForce() { CMAPTorsionForce::CMAPTorsionForce() : usePeriodic(false) {
} }
int CMAPTorsionForce::addMap(int size, const std::vector<double>& energy) { int CMAPTorsionForce::addMap(int size, const std::vector<double>& energy) {
...@@ -99,3 +99,11 @@ ForceImpl* CMAPTorsionForce::createImpl() const { ...@@ -99,3 +99,11 @@ ForceImpl* CMAPTorsionForce::createImpl() const {
void CMAPTorsionForce::updateParametersInContext(Context& context) { void CMAPTorsionForce::updateParametersInContext(Context& context) {
dynamic_cast<CMAPTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(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 @ 73183c61
...@@ -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) 2008-2013 Stanford University and the Authors. * * Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -84,15 +84,20 @@ ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integ ...@@ -84,15 +84,20 @@ ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integ
// Validate the list of properties. // Validate the list of properties.
const vector<string>& platformProperties = platform->getPropertyNames(); const vector<string>& platformProperties = platform->getPropertyNames();
map<string, string> validatedProperties;
for (map<string, string>::const_iterator iter = properties.begin(); iter != properties.end(); ++iter) { 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; bool valid = false;
for (int i = 0; i < (int) platformProperties.size(); i++) for (int i = 0; i < (int) platformProperties.size(); i++)
if (platformProperties[i] == iter->first) { if (platformProperties[i] == property) {
valid = true; valid = true;
break; break;
} }
if (!valid) if (!valid)
throw OpenMMException("Illegal property name: "+iter->first); throw OpenMMException("Illegal property name: "+iter->first);
validatedProperties[property] = iter->second;
} }
// Find the list of kernels required. // Find the list of kernels required.
...@@ -139,7 +144,7 @@ ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integ ...@@ -139,7 +144,7 @@ ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integ
for (int i = candidatePlatforms.size()-1; i >= 0; i--) { for (int i = candidatePlatforms.size()-1; i >= 0; i--) {
try { try {
this->platform = platform = candidatePlatforms[i].second; this->platform = platform = candidatePlatforms[i].second;
platform->contextCreated(*this, properties); platform->contextCreated(*this, validatedProperties);
break; break;
} }
catch (...) { catch (...) {
......
openmmapi/src/CustomAngleForce.cpp
View file @ 73183c61
...@@ -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) 2010 Stanford University and the Authors. * * Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -44,7 +44,7 @@ using std::string; ...@@ -44,7 +44,7 @@ using std::string;
using std::stringstream; using std::stringstream;
using std::vector; using std::vector;
CustomAngleForce::CustomAngleForce(const string& energy) : energyExpression(energy) { CustomAngleForce::CustomAngleForce(const string& energy) : energyExpression(energy), usePeriodic(false) {
} }
const string& CustomAngleForce::getEnergyFunction() const { const string& CustomAngleForce::getEnergyFunction() const {
...@@ -123,3 +123,11 @@ ForceImpl* CustomAngleForce::createImpl() const { ...@@ -123,3 +123,11 @@ ForceImpl* CustomAngleForce::createImpl() const {
void CustomAngleForce::updateParametersInContext(Context& context) { void CustomAngleForce::updateParametersInContext(Context& context) {
dynamic_cast<CustomAngleForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(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 @ 73183c61
...@@ -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) 2008-2009 Stanford University and the Authors. * * Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -44,7 +44,7 @@ using std::string; ...@@ -44,7 +44,7 @@ using std::string;
using std::stringstream; using std::stringstream;
using std::vector; using std::vector;
CustomBondForce::CustomBondForce(const string& energy) : energyExpression(energy) { CustomBondForce::CustomBondForce(const string& energy) : energyExpression(energy), usePeriodic(false) {
} }
const string& CustomBondForce::getEnergyFunction() const { const string& CustomBondForce::getEnergyFunction() const {
...@@ -121,3 +121,11 @@ ForceImpl* CustomBondForce::createImpl() const { ...@@ -121,3 +121,11 @@ ForceImpl* CustomBondForce::createImpl() const {
void CustomBondForce::updateParametersInContext(Context& context) { void CustomBondForce::updateParametersInContext(Context& context) {
dynamic_cast<CustomBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context)); dynamic_cast<CustomBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
} }
void CustomBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool CustomBondForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
openmmapi/src/CustomCentroidBondForce.cpp
View file @ 73183c61
...@@ -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) 2015 Stanford University and the Authors. * * Portions copyright (c) 2015-2016 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -48,7 +48,7 @@ using std::string; ...@@ -48,7 +48,7 @@ using std::string;
using std::stringstream; using std::stringstream;
using std::vector; using std::vector;
CustomCentroidBondForce::CustomCentroidBondForce(int numGroups, const string& energy) : groupsPerBond(numGroups), energyExpression(energy) { CustomCentroidBondForce::CustomCentroidBondForce(int numGroups, const string& energy) : groupsPerBond(numGroups), energyExpression(energy), usePeriodic(false) {
} }
CustomCentroidBondForce::~CustomCentroidBondForce() { CustomCentroidBondForce::~CustomCentroidBondForce() {
...@@ -173,3 +173,11 @@ ForceImpl* CustomCentroidBondForce::createImpl() const { ...@@ -173,3 +173,11 @@ ForceImpl* CustomCentroidBondForce::createImpl() const {
void CustomCentroidBondForce::updateParametersInContext(Context& context) { void CustomCentroidBondForce::updateParametersInContext(Context& context) {
dynamic_cast<CustomCentroidBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context)); dynamic_cast<CustomCentroidBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
} }
void CustomCentroidBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool CustomCentroidBondForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
openmmapi/src/CustomCompoundBondForce.cpp
View file @ 73183c61
...@@ -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) 2008-2014 Stanford University and the Authors. * * Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -48,7 +48,7 @@ using std::string; ...@@ -48,7 +48,7 @@ using std::string;
using std::stringstream; using std::stringstream;
using std::vector; 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), usePeriodic(false) {
} }
...@@ -176,3 +176,11 @@ ForceImpl* CustomCompoundBondForce::createImpl() const { ...@@ -176,3 +176,11 @@ ForceImpl* CustomCompoundBondForce::createImpl() const {
void CustomCompoundBondForce::updateParametersInContext(Context& context) { void CustomCompoundBondForce::updateParametersInContext(Context& context) {
dynamic_cast<CustomCompoundBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context)); dynamic_cast<CustomCompoundBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
} }
void CustomCompoundBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool CustomCompoundBondForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
openmmapi/src/CustomIntegrator.cpp
View file @ 73183c61
...@@ -248,21 +248,21 @@ int CustomIntegrator::addUpdateContextState() { ...@@ -248,21 +248,21 @@ int CustomIntegrator::addUpdateContextState() {
int CustomIntegrator::beginIfBlock(const string& expression) { int CustomIntegrator::beginIfBlock(const string& expression) {
if (owner != NULL) if (owner != NULL)
throw OpenMMException("The integrator cannot be modified after it is bound to a context"); throw OpenMMException("The integrator cannot be modified after it is bound to a context");
computations.push_back(ComputationInfo(BeginIfBlock, "", expression)); computations.push_back(ComputationInfo(IfBlockStart, "", expression));
return computations.size()-1; return computations.size()-1;
} }
int CustomIntegrator::beginWhileBlock(const string& expression) { int CustomIntegrator::beginWhileBlock(const string& expression) {
if (owner != NULL) if (owner != NULL)
throw OpenMMException("The integrator cannot be modified after it is bound to a context"); throw OpenMMException("The integrator cannot be modified after it is bound to a context");
computations.push_back(ComputationInfo(BeginWhileBlock, "", expression)); computations.push_back(ComputationInfo(WhileBlockStart, "", expression));
return computations.size()-1; return computations.size()-1;
} }
int CustomIntegrator::endBlock() { int CustomIntegrator::endBlock() {
if (owner != NULL) if (owner != NULL)
throw OpenMMException("The integrator cannot be modified after it is bound to a context"); throw OpenMMException("The integrator cannot be modified after it is bound to a context");
computations.push_back(ComputationInfo(EndBlock, "", "")); computations.push_back(ComputationInfo(BlockEnd, "", ""));
return computations.size()-1; return computations.size()-1;
} }
......
openmmapi/src/CustomIntegratorUtilities.cpp
View file @ 73183c61
...@@ -87,7 +87,7 @@ void CustomIntegratorUtilities::analyzeComputations(const ContextImpl& context, ...@@ -87,7 +87,7 @@ void CustomIntegratorUtilities::analyzeComputations(const ContextImpl& context,
for (int step = 0; step < numSteps; step++) { for (int step = 0; step < numSteps; step++) {
string expression; string expression;
integrator.getComputationStep(step, stepType[step], stepVariable[step], expression); integrator.getComputationStep(step, stepType[step], stepVariable[step], expression);
if (stepType[step] == CustomIntegrator::BeginIfBlock || stepType[step] == CustomIntegrator::BeginWhileBlock) { if (stepType[step] == CustomIntegrator::IfBlockStart || stepType[step] == CustomIntegrator::WhileBlockStart) {
// This step involves a condition. // This step involves a condition.
string lhs, rhs; string lhs, rhs;
...@@ -158,9 +158,9 @@ void CustomIntegratorUtilities::analyzeComputations(const ContextImpl& context, ...@@ -158,9 +158,9 @@ void CustomIntegratorUtilities::analyzeComputations(const ContextImpl& context,
vector<int> blockStart; vector<int> blockStart;
blockEnd.resize(numSteps, -1); blockEnd.resize(numSteps, -1);
for (int step = 0; step < numSteps; step++) { for (int step = 0; step < numSteps; step++) {
if (stepType[step] == CustomIntegrator::BeginIfBlock || stepType[step] == CustomIntegrator::BeginWhileBlock) if (stepType[step] == CustomIntegrator::IfBlockStart || stepType[step] == CustomIntegrator::WhileBlockStart)
blockStart.push_back(step); blockStart.push_back(step);
else if (stepType[step] == CustomIntegrator::EndBlock) { else if (stepType[step] == CustomIntegrator::BlockEnd) {
if (blockStart.size() == 0) { if (blockStart.size() == 0) {
stringstream error("CustomIntegrator: Unexpected end of block at computation "); stringstream error("CustomIntegrator: Unexpected end of block at computation ");
error << step; error << step;
...@@ -207,7 +207,7 @@ void CustomIntegratorUtilities::enumeratePaths(int firstStep, vector<int> steps, ...@@ -207,7 +207,7 @@ void CustomIntegratorUtilities::enumeratePaths(int firstStep, vector<int> steps,
jumps[step] = -1; jumps[step] = -1;
step = nextStep; step = nextStep;
} }
else if (stepType[step] == CustomIntegrator::BeginIfBlock) { else if (stepType[step] == CustomIntegrator::IfBlockStart) {
// Consider skipping the block. // Consider skipping the block.
enumeratePaths(blockEnd[step]+1, steps, jumps, blockEnd, stepType, needsForces, needsEnergy, invalidatesForces, forceGroup, computeBoth); enumeratePaths(blockEnd[step]+1, steps, jumps, blockEnd, stepType, needsForces, needsEnergy, invalidatesForces, forceGroup, computeBoth);
...@@ -216,7 +216,7 @@ void CustomIntegratorUtilities::enumeratePaths(int firstStep, vector<int> steps, ...@@ -216,7 +216,7 @@ void CustomIntegratorUtilities::enumeratePaths(int firstStep, vector<int> steps,
step++; step++;
} }
else if (stepType[step] == CustomIntegrator::BeginWhileBlock && jumps[step] != -2) { else if (stepType[step] == CustomIntegrator::WhileBlockStart && jumps[step] != -2) {
// Consider skipping the block. // Consider skipping the block.
enumeratePaths(blockEnd[step]+1, steps, jumps, blockEnd, stepType, needsForces, needsEnergy, invalidatesForces, forceGroup, computeBoth); enumeratePaths(blockEnd[step]+1, steps, jumps, blockEnd, stepType, needsForces, needsEnergy, invalidatesForces, forceGroup, computeBoth);
......
openmmapi/src/CustomTorsionForce.cpp
View file @ 73183c61
...@@ -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) 2010 Stanford University and the Authors. * * Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -44,7 +44,7 @@ using std::string; ...@@ -44,7 +44,7 @@ using std::string;
using std::stringstream; using std::stringstream;
using std::vector; using std::vector;
CustomTorsionForce::CustomTorsionForce(const string& energy) : energyExpression(energy) { CustomTorsionForce::CustomTorsionForce(const string& energy) : energyExpression(energy), usePeriodic(false) {
} }
const string& CustomTorsionForce::getEnergyFunction() const { const string& CustomTorsionForce::getEnergyFunction() const {
...@@ -125,3 +125,11 @@ ForceImpl* CustomTorsionForce::createImpl() const { ...@@ -125,3 +125,11 @@ ForceImpl* CustomTorsionForce::createImpl() const {
void CustomTorsionForce::updateParametersInContext(Context& context) { void CustomTorsionForce::updateParametersInContext(Context& context) {
dynamic_cast<CustomTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context)); dynamic_cast<CustomTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
} }
void CustomTorsionForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool CustomTorsionForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
openmmapi/src/HarmonicAngleForce.cpp
View file @ 73183c61
...@@ -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) 2008-2009 Stanford University and the Authors. * * Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -37,7 +37,7 @@ ...@@ -37,7 +37,7 @@
using namespace OpenMM; using namespace OpenMM;
HarmonicAngleForce::HarmonicAngleForce() { HarmonicAngleForce::HarmonicAngleForce() : usePeriodic(false) {
} }
int HarmonicAngleForce::addAngle(int particle1, int particle2, int particle3, double angle, double k) { int HarmonicAngleForce::addAngle(int particle1, int particle2, int particle3, double angle, double k) {
...@@ -70,3 +70,11 @@ ForceImpl* HarmonicAngleForce::createImpl() const { ...@@ -70,3 +70,11 @@ ForceImpl* HarmonicAngleForce::createImpl() const {
void HarmonicAngleForce::updateParametersInContext(Context& context) { void HarmonicAngleForce::updateParametersInContext(Context& context) {
dynamic_cast<HarmonicAngleForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context)); dynamic_cast<HarmonicAngleForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
} }
void HarmonicAngleForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool HarmonicAngleForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
openmmapi/src/HarmonicBondForce.cpp
View file @ 73183c61
...@@ -37,7 +37,7 @@ ...@@ -37,7 +37,7 @@
using namespace OpenMM; using namespace OpenMM;
HarmonicBondForce::HarmonicBondForce() { HarmonicBondForce::HarmonicBondForce() : usePeriodic(false) {
} }
int HarmonicBondForce::addBond(int particle1, int particle2, double length, double k) { int HarmonicBondForce::addBond(int particle1, int particle2, double length, double k) {
...@@ -68,3 +68,11 @@ ForceImpl* HarmonicBondForce::createImpl() const { ...@@ -68,3 +68,11 @@ ForceImpl* HarmonicBondForce::createImpl() const {
void HarmonicBondForce::updateParametersInContext(Context& context) { void HarmonicBondForce::updateParametersInContext(Context& context) {
dynamic_cast<HarmonicBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context)); dynamic_cast<HarmonicBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
} }
void HarmonicBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool HarmonicBondForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
openmmapi/src/LocalEnergyMinimizer.cpp
View file @ 73183c61
...@@ -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) 2010-2012 Stanford University and the Authors. * * Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -108,7 +108,8 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI ...@@ -108,7 +108,8 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
if (x == NULL) if (x == NULL)
throw OpenMMException("LocalEnergyMinimizer: Failed to allocate memory"); throw OpenMMException("LocalEnergyMinimizer: Failed to allocate memory");
double constraintTol = context.getIntegrator().getConstraintTolerance(); double constraintTol = context.getIntegrator().getConstraintTolerance();
double k = tolerance/constraintTol; double workingConstraintTol = max(1e-4, constraintTol);
double k = tolerance/workingConstraintTol;
// Initialize the minimizer. // Initialize the minimizer.
...@@ -121,7 +122,7 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI ...@@ -121,7 +122,7 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
// Make sure the initial configuration satisfies all constraints. // Make sure the initial configuration satisfies all constraints.
context.applyConstraints(constraintTol); context.applyConstraints(workingConstraintTol);
// Record the initial positions and determine a normalization constant for scaling the tolerance. // Record the initial positions and determine a normalization constant for scaling the tolerance.
...@@ -162,14 +163,14 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI ...@@ -162,14 +163,14 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
if (error > maxError) if (error > maxError)
maxError = error; maxError = error;
} }
if (maxError <= constraintTol) if (maxError <= workingConstraintTol)
break; // All constraints are satisfied. break; // All constraints are satisfied.
context.setPositions(initialPos); context.setPositions(initialPos);
if (maxError >= prevMaxError) if (maxError >= prevMaxError)
break; // Further tightening the springs doesn't seem to be helping, so just give up. break; // Further tightening the springs doesn't seem to be helping, so just give up.
prevMaxError = maxError; prevMaxError = maxError;
k *= 10; k *= 10;
if (maxError > 100*constraintTol) { if (maxError > 100*workingConstraintTol) {
// We've gotten far enough from a valid state that we might have trouble getting // We've gotten far enough from a valid state that we might have trouble getting
// back, so reset to the original positions. // back, so reset to the original positions.
...@@ -181,5 +182,11 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI ...@@ -181,5 +182,11 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
} }
} }
lbfgs_free(x); lbfgs_free(x);
// If necessary, do a final constraint projection to make sure they are satisfied
// to the full precision requested by the user.
if (constraintTol < workingConstraintTol)
context.applyConstraints(workingConstraintTol);
} }
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment