Update to files corruptedd in r2814

openmmapi/src/GBVIForce.cpp

-Vim: Warning: Output is not to a terminal
-[?1049h[?1h=[?12;25h[?12l[?25h[?25l"svn-commit.tmp" 15L, 601C  1 
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-  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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                                                                                                                                                                                                                 ~                                                                                                                                                                                                                                         ~                                                                                                                                                                                                                                         ~                                                                                                                                                                                                                                         ~                                                                                         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                                                                               ~                                                                                                                                                                                                                                         ~                                                                                                                                                                                                                                         ~                                                                                                                                                                                                                                         ~                                                                                                                                                                                                                           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-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);
+}