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Commit a2674e83 authored by Mark Friedrichs's avatar Mark Friedrichs
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Mods for GB/VI switching of Born radii

parent 38839771
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openmmapi/include/openmm/GBVIForce.h
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openmmapi/src/GBVIForce.cpp
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/* -------------------------------------------------------------------------- *
* 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;
}
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);
}
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
......
platforms/cuda/src/CudaKernels.cpp
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platforms/cuda/src/kernels/cudatypes.h
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platforms/cuda/src/kernels/gpu.cpp
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platforms/cuda/src/kernels/gputypes.h
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platforms/cuda/src/kernels/kForces.cu
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