Skip to content

GitLab

Commit 6403d1ec authored by Jason Swails's avatar Jason Swails
Browse files

dos2unix AmoebaVdwForce.h

parent 197d7762
Hide whitespace changes
Inline Side-by-side
Showing with 263 additions and 263 deletions
plugins/amoeba/openmmapi/include/openmm/AmoebaVdwForce.h
View file @ 6403d1ec
#ifndef OPENMM_AMOEBA_VDW_FORCE_H_
#define OPENMM_AMOEBA_VDW_FORCE_H_
/* -------------------------------------------------------------------------- *
* OpenMMAmoeba *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Authors: Mark Friedrichs, Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/Force.h"
#include "internal/windowsExportAmoeba.h"
#include <vector>
namespace OpenMM {
/**
* This class implements a buffered 14-7 potential used to model van der Waals forces.
*
* To use it, create an AmoebaVdwForce object then call addParticle() once for each particle. After
* a particle has been added, you can modify its force field parameters by calling setParticleParameters().
* This will have no effect on Contexts that already exist unless you call updateParametersInContext().
*
* A unique feature of this class is that the interaction site for a particle does not need to be
* exactly at the particle's location. Instead, it can be placed a fraction of the distance from that
* particle to another one. This is typically done for hydrogens to place the interaction site slightly
* closer to the parent atom. The fraction is known as the "reduction factor", since it reduces the distance
* from the parent atom to the interaction site.
*/
class OPENMM_EXPORT_AMOEBA AmoebaVdwForce : public Force {
public:
/**
* This is an enumeration of the different methods that may be used for handling long range nonbonded forces.
*/
enum NonbondedMethod {
/**
* No cutoff is applied to nonbonded interactions. The full set of N^2 interactions is computed exactly.
* This necessarily means that periodic boundary conditions cannot be used. This is the default.
*/
NoCutoff = 0,
/**
* Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic copy of
* each other particle. Interactions beyond the cutoff distance are ignored.
*/
CutoffPeriodic = 1,
};
/**
* Create an Amoeba VdwForce.
*/
AmoebaVdwForce();
/**
* Get the number of particles
*/
int getNumParticles() const {
return parameters.size();
}
/**
* Set the force field parameters for a vdw particle.
*
* @param particleIndex the particle index
* @param parentIndex the index of the parent particle
* @param sigma vdw sigma
* @param epsilon vdw epsilon
* @param reductionFactor the fraction of the distance along the line from the parent particle to this particle
* at which the interaction site should be placed
*/
void setParticleParameters(int particleIndex, int parentIndex, double sigma, double epsilon, double reductionFactor);
/**
* Get the force field parameters for a vdw particle.
*
* @param particleIndex the particle index
* @param parentIndex the index of the parent particle
* @param sigma vdw sigma
* @param epsilon vdw epsilon
* @param reductionFactor the fraction of the distance along the line from the parent particle to this particle
* at which the interaction site should be placed
*/
void getParticleParameters(int particleIndex, int& parentIndex, double& sigma, double& epsilon, double& reductionFactor) const;
/**
* Add the force field parameters for a vdw particle.
*
* @param parentIndex the index of the parent particle
* @param sigma vdw sigma
* @param epsilon vdw epsilon
* @param reductionFactor the fraction of the distance along the line from the parent particle to this particle
* at which the interaction site should be placed
* @return index of added particle
*/
int addParticle(int parentIndex, double sigma, double epsilon, double reductionFactor);
/**
* Set sigma combining rule
*
* @param sigmaCombiningRule sigma combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN'
*/
void setSigmaCombiningRule(const std::string& sigmaCombiningRule);
/**
* Get sigma combining rule
*
* @return sigmaCombiningRule sigma combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN'
*/
const std::string& getSigmaCombiningRule(void) const;
/**
* Set epsilon combining rule
*
* @param epsilonCombiningRule epsilon combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'HHG'
*/
void setEpsilonCombiningRule(const std::string& epsilonCombiningRule);
/**
* Get epsilon combining rule
*
* @return epsilonCombiningRule epsilon combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'HHG'
*/
const std::string& getEpsilonCombiningRule(void) const;
/**
* Get whether to add a contribution to the energy that approximately represents the effect of VdW
* interactions beyond the cutoff distance. The energy depends on the volume of the periodic box, and is only
* applicable when periodic boundary conditions are used. When running simulations at constant pressure, adding
* this contribution can improve the quality of results.
*/
bool getUseDispersionCorrection() const {
return useDispersionCorrection;
}
/**
* Set whether to add a contribution to the energy that approximately represents the effect of VdW
* interactions beyond the cutoff distance. The energy depends on the volume of the periodic box, and is only
* applicable when periodic boundary conditions are used. When running simulations at constant pressure, adding
* this contribution can improve the quality of results.
*/
void setUseDispersionCorrection(bool useCorrection) {
useDispersionCorrection = useCorrection;
}
/**
* Set exclusions for specified particle
*
* @param particleIndex particle index
* @param exclusions vector of exclusions
*/
void setParticleExclusions(int particleIndex, const std::vector<int>& exclusions);
/**
* Get exclusions for specified particle
*
* @param particleIndex particle index
* @param exclusions vector of exclusions
*/
void getParticleExclusions(int particleIndex, std::vector<int>& exclusions) const;
/**
* Set the cutoff distance.
*/
void setCutoff(double cutoff);
/**
* Get the cutoff distance.
*/
double getCutoff() const;
/**
* Get the method used for handling long range nonbonded interactions.
*/
NonbondedMethod getNonbondedMethod() const;
/**
* Set the method used for handling long range nonbonded interactions.
*/
void setNonbondedMethod(NonbondedMethod method);
/**
* Update the per-particle parameters in a Context to match those stored in this Force object. This method provides
* an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
* Simply call setParticleParameters() to modify this object's parameters, then call updateParametersInContext()
* to copy them over to the Context.
*
* The only information this method updates is the values of per-particle parameters. All other aspects of the Force
* (the nonbonded method, the cutoff distance, etc.) are unaffected and can only be changed by reinitializing the Context.
*/
void updateParametersInContext(Context& context);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns true if nonbondedMethod uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return nonbondedMethod == AmoebaVdwForce::CutoffPeriodic;
}
protected:
ForceImpl* createImpl() const;
private:
class VdwInfo;
NonbondedMethod nonbondedMethod;
double cutoff;
bool useDispersionCorrection;
std::string sigmaCombiningRule;
std::string epsilonCombiningRule;
std::vector< std::vector<int> > exclusions;
std::vector<VdwInfo> parameters;
std::vector< std::vector< std::vector<double> > > sigEpsTable;
};
/**
* This is an internal class used to record information about a particle.
* @private
*/
class AmoebaVdwForce::VdwInfo {
public:
int parentIndex;
double reductionFactor, sigma, epsilon, cutoff;
VdwInfo() {
parentIndex = -1;
reductionFactor = 0.0;
sigma = 1.0;
epsilon = 0.0;
}
VdwInfo(int parentIndex, double sigma, double epsilon, double reductionFactor) :
parentIndex(parentIndex), reductionFactor(reductionFactor), sigma(sigma), epsilon(epsilon) {
}
};
} // namespace OpenMM
#endif /*OPENMM_AMOEBA_VDW_FORCE_H_*/
#ifndef OPENMM_AMOEBA_VDW_FORCE_H_
#define OPENMM_AMOEBA_VDW_FORCE_H_
/* -------------------------------------------------------------------------- *
* OpenMMAmoeba *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Authors: Mark Friedrichs, Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/Force.h"
#include "internal/windowsExportAmoeba.h"
#include <vector>
namespace OpenMM {
/**
* This class implements a buffered 14-7 potential used to model van der Waals forces.
*
* To use it, create an AmoebaVdwForce object then call addParticle() once for each particle. After
* a particle has been added, you can modify its force field parameters by calling setParticleParameters().
* This will have no effect on Contexts that already exist unless you call updateParametersInContext().
*
* A unique feature of this class is that the interaction site for a particle does not need to be
* exactly at the particle's location. Instead, it can be placed a fraction of the distance from that
* particle to another one. This is typically done for hydrogens to place the interaction site slightly
* closer to the parent atom. The fraction is known as the "reduction factor", since it reduces the distance
* from the parent atom to the interaction site.
*/
class OPENMM_EXPORT_AMOEBA AmoebaVdwForce : public Force {
public:
/**
* This is an enumeration of the different methods that may be used for handling long range nonbonded forces.
*/
enum NonbondedMethod {
/**
* No cutoff is applied to nonbonded interactions. The full set of N^2 interactions is computed exactly.
* This necessarily means that periodic boundary conditions cannot be used. This is the default.
*/
NoCutoff = 0,
/**
* Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic copy of
* each other particle. Interactions beyond the cutoff distance are ignored.
*/
CutoffPeriodic = 1,
};
/**
* Create an Amoeba VdwForce.
*/
AmoebaVdwForce();
/**
* Get the number of particles
*/
int getNumParticles() const {
return parameters.size();
}
/**
* Set the force field parameters for a vdw particle.
*
* @param particleIndex the particle index
* @param parentIndex the index of the parent particle
* @param sigma vdw sigma
* @param epsilon vdw epsilon
* @param reductionFactor the fraction of the distance along the line from the parent particle to this particle
* at which the interaction site should be placed
*/
void setParticleParameters(int particleIndex, int parentIndex, double sigma, double epsilon, double reductionFactor);
/**
* Get the force field parameters for a vdw particle.
*
* @param particleIndex the particle index
* @param parentIndex the index of the parent particle
* @param sigma vdw sigma
* @param epsilon vdw epsilon
* @param reductionFactor the fraction of the distance along the line from the parent particle to this particle
* at which the interaction site should be placed
*/
void getParticleParameters(int particleIndex, int& parentIndex, double& sigma, double& epsilon, double& reductionFactor) const;
/**
* Add the force field parameters for a vdw particle.
*
* @param parentIndex the index of the parent particle
* @param sigma vdw sigma
* @param epsilon vdw epsilon
* @param reductionFactor the fraction of the distance along the line from the parent particle to this particle
* at which the interaction site should be placed
* @return index of added particle
*/
int addParticle(int parentIndex, double sigma, double epsilon, double reductionFactor);
/**
* Set sigma combining rule
*
* @param sigmaCombiningRule sigma combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN'
*/
void setSigmaCombiningRule(const std::string& sigmaCombiningRule);
/**
* Get sigma combining rule
*
* @return sigmaCombiningRule sigma combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'CUBIC-MEAN'
*/
const std::string& getSigmaCombiningRule(void) const;
/**
* Set epsilon combining rule
*
* @param epsilonCombiningRule epsilon combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'HHG'
*/
void setEpsilonCombiningRule(const std::string& epsilonCombiningRule);
/**
* Get epsilon combining rule
*
* @return epsilonCombiningRule epsilon combining rule: 'ARITHMETIC', 'GEOMETRIC'. 'HARMONIC', 'HHG'
*/
const std::string& getEpsilonCombiningRule(void) const;
/**
* Get whether to add a contribution to the energy that approximately represents the effect of VdW
* interactions beyond the cutoff distance. The energy depends on the volume of the periodic box, and is only
* applicable when periodic boundary conditions are used. When running simulations at constant pressure, adding
* this contribution can improve the quality of results.
*/
bool getUseDispersionCorrection() const {
return useDispersionCorrection;
}
/**
* Set whether to add a contribution to the energy that approximately represents the effect of VdW
* interactions beyond the cutoff distance. The energy depends on the volume of the periodic box, and is only
* applicable when periodic boundary conditions are used. When running simulations at constant pressure, adding
* this contribution can improve the quality of results.
*/
void setUseDispersionCorrection(bool useCorrection) {
useDispersionCorrection = useCorrection;
}
/**
* Set exclusions for specified particle
*
* @param particleIndex particle index
* @param exclusions vector of exclusions
*/
void setParticleExclusions(int particleIndex, const std::vector<int>& exclusions);
/**
* Get exclusions for specified particle
*
* @param particleIndex particle index
* @param exclusions vector of exclusions
*/
void getParticleExclusions(int particleIndex, std::vector<int>& exclusions) const;
/**
* Set the cutoff distance.
*/
void setCutoff(double cutoff);
/**
* Get the cutoff distance.
*/
double getCutoff() const;
/**
* Get the method used for handling long range nonbonded interactions.
*/
NonbondedMethod getNonbondedMethod() const;
/**
* Set the method used for handling long range nonbonded interactions.
*/
void setNonbondedMethod(NonbondedMethod method);
/**
* Update the per-particle parameters in a Context to match those stored in this Force object. This method provides
* an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
* Simply call setParticleParameters() to modify this object's parameters, then call updateParametersInContext()
* to copy them over to the Context.
*
* The only information this method updates is the values of per-particle parameters. All other aspects of the Force
* (the nonbonded method, the cutoff distance, etc.) are unaffected and can only be changed by reinitializing the Context.
*/
void updateParametersInContext(Context& context);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns true if nonbondedMethod uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return nonbondedMethod == AmoebaVdwForce::CutoffPeriodic;
}
protected:
ForceImpl* createImpl() const;
private:
class VdwInfo;
NonbondedMethod nonbondedMethod;
double cutoff;
bool useDispersionCorrection;
std::string sigmaCombiningRule;
std::string epsilonCombiningRule;
std::vector< std::vector<int> > exclusions;
std::vector<VdwInfo> parameters;
std::vector< std::vector< std::vector<double> > > sigEpsTable;
};
/**
* This is an internal class used to record information about a particle.
* @private
*/
class AmoebaVdwForce::VdwInfo {
public:
int parentIndex;
double reductionFactor, sigma, epsilon, cutoff;
VdwInfo() {
parentIndex = -1;
reductionFactor = 0.0;
sigma = 1.0;
epsilon = 0.0;
}
VdwInfo(int parentIndex, double sigma, double epsilon, double reductionFactor) :
parentIndex(parentIndex), reductionFactor(reductionFactor), sigma(sigma), epsilon(epsilon) {
}
};
} // namespace OpenMM
#endif /*OPENMM_AMOEBA_VDW_FORCE_H_*/
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