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Commit d2365200 authored by Mark Friedrichs's avatar Mark Friedrichs
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Update to files corruptedd in r2814

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openmmapi/include/openmm/GBVIForce.h
View file @ d2365200
Vim: Warning: Output is not to a terminal
[?1049h[?1h=[?12;25h[?12l[?25h[?25l"svn-commit.tmp" 15L, 601C 1
2 --This line, and those below, will be ignored--
 3
4 M plugins/amoeba/platforms/cuda/src/AmoebaCudaKernelFactory.cpp
 5 M plugins/freeEnergy/platforms/reference/src/gbsa/CpuGBVISoftcore.cpp
 6 M openmmapi/include/openmm/GBVIForce.h
 7 M openmmapi/src/GBVIForce.cpp
 8 M olla/src/Platform.cpp
 9 M platforms/opencl/src/OpenCLContext.h
 10 M platforms/cuda/src/CudaKernels.cpp
 11 M platforms/cuda/src/kernels/kCalculateGBVIBornSum.cu
 12 M platforms/cuda/src/kernels/gputypes.h
 13 M platforms/cuda/src/kernels/cudatypes.h
 14 M platforms/cuda/src/kernels/kForces.cu
 15 M platforms/cuda/src/kernels/gpu.cpp
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Log message unchanged or not specified
a)bort, c)ontinue, e)dit
#ifndef OPENMM_GBVIFORCEFIELD_H_
#define OPENMM_GBVIFORCEFIELD_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "Force.h"
#include <vector>
#include "internal/windowsExport.h"
namespace OpenMM {
/**
* This class implements an implicit solvation force using the GB/VI model.
* <p>
* To use this class, create a GBVIForce object, then call addParticle() once for each particle in the
* System to define its parameters. The number of particles for which you define GB/VI parameters must
* be exactly equal to the number of particles in the System, or else an exception will be thrown when you
* try to create a Context. After a particle has been added, you can modify its force field parameters
* by calling setParticleParameters().
*/
class OPENMM_EXPORT GBVIForce : 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,
/**
* Interactions beyond the cutoff distance are ignored.
*/
CutoffNonPeriodic = 1,
/**
* 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 = 2,
};
/**
* This is an enumeration of the different methods that may be used for scaling of the Born radii.
*/
enum BornRadiusScalingMethod {
/**
* No scaling method is applied.
*/
NoScaling = 0,
/**
* Use the method outlined in Proteins 55, 383-394 (2004), Eq. 6
*/
Tanh = 1,
/**
* Use quintic spline scaling function
*/
QuinticSpline = 2
};
/*
* Create a GBVIForce.
*/
GBVIForce();
/**
* Get the number of particles in the system.
*/
int getNumParticles() const {
return particles.size();
}
/**
* Add the GB/VI parameters for a particle. This should be called once for each particle
* in the System. When it is called for the i'th time, it specifies the parameters for the i'th particle.
*
* @param charge the charge of the particle, measured in units of the proton charge
* @param radius the GB/VI radius of the particle, measured in nm
* @param gamma the gamma parameter
* @return the index of the particle that was added
*/
int addParticle(double charge, double radius, double gamma);
/**
* Get the force field parameters for a particle.
*
* @param index the index of the particle for which to get parameters
* @param charge the charge of the particle, measured in units of the proton charge
* @param radius the GBSA radius of the particle, measured in nm
* @param gamma the gamma parameter
*/
void getParticleParameters(int index, double& charge, double& radius, double& gamma) const;
/**
* Set the force field parameters for a particle.
*
* @param index the index of the particle for which to set parameters
* @param charge the charge of the particle, measured in units of the proton charge
* @param radius the GB/VI radius of the particle, measured in nm
* @param gamma the gamma parameter
*/
void setParticleParameters(int index, double charge, double radius, double gamma);
/**
* Add a bond
*
* @param particle1 the index of the first particle
* @param particle2 the index of the second particle
* @param distance the distance between the two particles, measured in nm
* @return the index of the bond that was added
*/
int addBond(int particle1, int particle2, double distance);
/**
* Get the parameters defining a bond
*
* @param index the index of the bond for which to get parameters
* @param particle1 the index of the first particle involved in the bond
* @param particle2 the index of the second particle involved in the bond
* @param distance the distance between the two particles, measured in nm
*/
void getBondParameters(int index, int& particle1, int& particle2, double& distance) const;
/**
* Set 1-2 bonds
*
* @param index index of the bond for which to set parameters
* @param particle1 index of first atom in bond
* @param particle2 index of second atom in bond
* @param bondLength bond length
*/
void setBondParameters( int index, int particle1, int particle2, double bondLength);
/**
* Get number of bonds
*
* @return number of bonds
*/
int getNumBonds( void ) const;
/**
* Get the dielectric constant for the solvent.
*/
double getSolventDielectric() const {
return solventDielectric;
}
/**
* Set the dielectric constant for the solvent.
*/
void setSolventDielectric(double dielectric) {
solventDielectric = dielectric;
}
/**
* Get the dielectric constant for the solute.
*/
double getSoluteDielectric() const {
return soluteDielectric;
}
/**
* Set the dielectric constant for the solute.
*/
void setSoluteDielectric(double dielectric) {
soluteDielectric = dielectric;
}
/**
* 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);
/**
* Get the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use
* is NoCutoff, this value will have no effect.
*
* @return the cutoff distance, measured in nm
*/
double getCutoffDistance() const;
/**
* Set the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use
* is NoCutoff, this value will have no effect.
*
* @param distance the cutoff distance, measured in nm
*/
void setCutoffDistance(double distance);
/**
* Get Born radius scalling method
*/
GBVIForce::BornRadiusScalingMethod getBornRadiusScalingMethod( void ) const;
/**
* Set Born radius scalling method
*/
void setBornRadiusScalingMethod( BornRadiusScalingMethod method);
/**
* Get the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)
*/
double getQuinticLowerLimitFactor( void ) const;
/**
* Set the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)
*/
void setQuinticLowerLimitFactor(double quinticLowerLimitFactor );
/**
* Get the upper limit used in the quintic spline scaling method (typically 0.5-0.8)
*/
double getQuinticUpperBornRadiusLimit( void ) const;
/**
* Set the upper limit used in the quintic spline scaling method (typically 0.008)
*/
void setQuinticUpperBornRadiusLimit(double quinticUpperBornRadiusLimit);
protected:
ForceImpl* createImpl();
private:
class ParticleInfo;
NonbondedMethod nonbondedMethod;
double cutoffDistance, solventDielectric, soluteDielectric;
BornRadiusScalingMethod scalingMethod;
double quinticLowerLimitFactor, quinticUpperBornRadiusLimit;
class BondInfo;
std::vector<ParticleInfo> particles;
std::vector<BondInfo> bonds;
};
/**
* This is an internal class used to record information about a particle.
* @private
*/
class GBVIForce::ParticleInfo {
public:
double charge, radius, gamma;
ParticleInfo() {
charge = radius = gamma = 0.0;
}
ParticleInfo(double charge, double radius, double gamma) :
charge(charge), radius(radius), gamma(gamma) {
}
};
/**
* This is an internal class used to record information about a bond.
* @private
*/
class GBVIForce::BondInfo {
public:
int particle1, particle2;
double bondLength;
BondInfo() {
bondLength = 0.0;
particle1 = -1;
particle2 = -1;
}
BondInfo(int atomIndex1, int atomIndex2, double bondLength) :
particle1(atomIndex1), particle2(atomIndex2), bondLength(bondLength) {
}
};
} // namespace OpenMM
#endif /*OPENMM_GBVIFORCEFIELD_H_*/
openmmapi/src/GBVIForce.cpp
View file @ d2365200
Vim: Warning: Output is not to a terminal
[?1049h[?1h=[?12;25h[?12l[?25h[?25l"svn-commit.tmp" 15L, 601C 1
2 --This line, and those below, will be ignored--
 3
4 M plugins/amoeba/platforms/cuda/src/AmoebaCudaKernelFactory.cpp
 5 M plugins/freeEnergy/platforms/reference/src/gbsa/CpuGBVISoftcore.cpp
 6 M openmmapi/include/openmm/GBVIForce.h
 7 M openmmapi/src/GBVIForce.cpp
 8 M olla/src/Platform.cpp
 9 M platforms/opencl/src/OpenCLContext.h
 10 M platforms/cuda/src/CudaKernels.cpp
 11 M platforms/cuda/src/kernels/kCalculateGBVIBornSum.cu
 12 M platforms/cuda/src/kernels/gputypes.h
 13 M platforms/cuda/src/kernels/cudatypes.h
 14 M platforms/cuda/src/kernels/kForces.cu
 15 M platforms/cuda/src/kernels/gpu.cpp
~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ 1,0-1All[?12l[?25h[?25l:[?12l[?25hq![?25l[?1l>[?12l[?25h[?1049l
Log message unchanged or not specified
a)bort, c)ontinue, e)dit
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/Force.h"
#include "openmm/OpenMMException.h"
#include "openmm/GBVIForce.h"
#include "openmm/internal/GBVIForceImpl.h"
#include <sstream>
using namespace OpenMM;
GBVIForce::GBVIForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0), solventDielectric(78.3), soluteDielectric(1.0) {
}
int GBVIForce::addParticle(double charge, double radius, double gamma) {
particles.push_back(ParticleInfo(charge, radius, gamma));
return particles.size()-1;
}
void GBVIForce::getParticleParameters(int index, double& charge, double& radius, double& gamma) const {
charge = particles[index].charge;
radius = particles[index].radius;
gamma = particles[index].gamma;
}
void GBVIForce::setParticleParameters(int index, double charge, double radius, double gamma) {
particles[index].charge = charge;
particles[index].radius = radius;
particles[index].gamma = gamma;
}
GBVIForce::NonbondedMethod GBVIForce::getNonbondedMethod() const {
return nonbondedMethod;
}
void GBVIForce::setNonbondedMethod(NonbondedMethod method) {
nonbondedMethod = method;
}
double GBVIForce::getCutoffDistance() const {
return cutoffDistance;
}
void GBVIForce::setCutoffDistance(double distance) {
cutoffDistance = distance;
}
GBVIForce::BornRadiusScalingMethod GBVIForce::getBornRadiusScalingMethod( void ) const {
return scalingMethod;
}
void GBVIForce::setBornRadiusScalingMethod(BornRadiusScalingMethod method) {
scalingMethod = method;
}
double GBVIForce::getQuinticLowerLimitFactor( void ) const {
return quinticLowerLimitFactor;
}
void GBVIForce::setQuinticLowerLimitFactor(double inputQuinticLowerLimitFactor ){
quinticLowerLimitFactor = inputQuinticLowerLimitFactor;
}
double GBVIForce::getQuinticUpperBornRadiusLimit( void ) const {
return quinticUpperBornRadiusLimit;
}
void GBVIForce::setQuinticUpperBornRadiusLimit(double inputQuinticUpperBornRadiusLimit){
quinticUpperBornRadiusLimit = inputQuinticUpperBornRadiusLimit;
}
int GBVIForce::addBond(int particle1, int particle2, double bondLength) {
bonds.push_back(BondInfo(particle1, particle2, bondLength));
return bonds.size()-1;
}
void GBVIForce::setBondParameters( int index, int particle1, int particle2, double bondLength) {
bonds[index].particle1 = particle1;
bonds[index].particle2 = particle2;
bonds[index].bondLength = bondLength;
}
int GBVIForce::getNumBonds( void ) const {
return (int) bonds.size();
}
void GBVIForce::getBondParameters(int index, int& bondIndex1, int& bondIndex2, double& bondLength) const {
bondIndex1 = bonds[index].particle1;
bondIndex2 = bonds[index].particle2;
bondLength = bonds[index].bondLength;
}
ForceImpl* GBVIForce::createImpl() {
return new GBVIForceImpl(*this);
}
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