/* -------------------------------------------------------------------------- * * 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) 2012-2017 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/VirtualSite.h" #include "openmm/OpenMMException.h" #include #include using namespace OpenMM; using namespace std; void VirtualSite::setParticles(const vector& particleIndices) { particles = particleIndices; } int VirtualSite::getNumParticles() const { return particles.size(); } int VirtualSite::getParticle(int particle) const { return particles[particle]; } TwoParticleAverageSite::TwoParticleAverageSite(int particle1, int particle2, double weight1, double weight2) : weight1(weight1), weight2(weight2) { vector particles(2); particles[0] = particle1; particles[1] = particle2; setParticles(particles); } double TwoParticleAverageSite::getWeight(int particle) const { if (particle == 0) return weight1; if (particle == 1) return weight2; throw OpenMMException("Illegal index for particle"); } ThreeParticleAverageSite::ThreeParticleAverageSite(int particle1, int particle2, int particle3, double weight1, double weight2, double weight3) : weight1(weight1), weight2(weight2), weight3(weight3) { vector particles(3); particles[0] = particle1; particles[1] = particle2; particles[2] = particle3; setParticles(particles); } double ThreeParticleAverageSite::getWeight(int particle) const { if (particle == 0) return weight1; if (particle == 1) return weight2; if (particle == 2) return weight3; throw OpenMMException("Illegal index for particle"); } OutOfPlaneSite::OutOfPlaneSite(int particle1, int particle2, int particle3, double weight12, double weight13, double weightCross) : weight12(weight12), weight13(weight13), weightCross(weightCross) { vector particles(3); particles[0] = particle1; particles[1] = particle2; particles[2] = particle3; setParticles(particles); } double OutOfPlaneSite::getWeight12() const { return weight12; } double OutOfPlaneSite::getWeight13() const { return weight13; } double OutOfPlaneSite::getWeightCross() const { return weightCross; } LocalCoordinatesSite::LocalCoordinatesSite(const vector& particles, const vector& originWeights, const vector& xWeights, const vector& yWeights, const Vec3& localPosition) : originWeights(originWeights), xWeights(xWeights), yWeights(yWeights), localPosition(localPosition) { int numParticles = particles.size(); if (numParticles < 2) throw OpenMMException("LocalCoordinatesSite: Must depend on at least two other particles"); if (originWeights.size() != numParticles || xWeights.size() != numParticles || yWeights.size() != numParticles) throw OpenMMException("LocalCoordinatesSite: Number of weights does not match number of particles"); double originSum = 0, xSum = 0, ySum = 0; for (int i = 0; i < numParticles; i++) { originSum += originWeights[i]; xSum += xWeights[i]; ySum += yWeights[i]; } if (fabs(originSum-1.0) > 1e-6) throw OpenMMException("LocalCoordinatesSite: Weights for computing origin must add to 1"); if (fabs(xSum) > 1e-6) throw OpenMMException("LocalCoordinatesSite: Weights for computing x axis must add to 0"); if (fabs(ySum) > 1e-6) throw OpenMMException("LocalCoordinatesSite: Weights for computing y axis must add to 0"); setParticles(particles); } LocalCoordinatesSite::LocalCoordinatesSite(int particle1, int particle2, int particle3, const Vec3& originWeights, const Vec3& xWeights, const Vec3& yWeights, const Vec3& localPosition) : localPosition(localPosition) { if (fabs(originWeights[0]+originWeights[1]+originWeights[2]-1.0) > 1e-6) throw OpenMMException("LocalCoordinatesSite: Weights for computing origin must add to 1"); if (fabs(xWeights[0]+xWeights[1]+xWeights[2]) > 1e-6) throw OpenMMException("LocalCoordinatesSite: Weights for computing x axis must add to 0"); if (fabs(yWeights[0]+yWeights[1]+yWeights[2]) > 1e-6) throw OpenMMException("LocalCoordinatesSite: Weights for computing y axis must add to 0"); vector particles(3); particles[0] = particle1; particles[1] = particle2; particles[2] = particle3; setParticles(particles); this->originWeights.push_back(originWeights[0]); this->originWeights.push_back(originWeights[1]); this->originWeights.push_back(originWeights[2]); this->xWeights.push_back(xWeights[0]); this->xWeights.push_back(xWeights[1]); this->xWeights.push_back(xWeights[2]); this->yWeights.push_back(yWeights[0]); this->yWeights.push_back(yWeights[1]); this->yWeights.push_back(yWeights[2]); } void LocalCoordinatesSite::getOriginWeights(vector& weights) const { weights = originWeights; } Vec3 LocalCoordinatesSite::getOriginWeights() const { if (originWeights.size() != 3) throw OpenMMException("LocalCoordinatesSite: This version of getOriginWeights() requires the site to depend on three particles"); return Vec3(originWeights[0], originWeights[1], originWeights[2]); } void LocalCoordinatesSite::getXWeights(vector& weights) const { weights = xWeights; } Vec3 LocalCoordinatesSite::getXWeights() const { if (xWeights.size() != 3) throw OpenMMException("LocalCoordinatesSite: This version of getXWeights() requires the site to depend on three particles"); return Vec3(xWeights[0], xWeights[1], xWeights[2]); } void LocalCoordinatesSite::getYWeights(vector& weights) const { weights = yWeights; } Vec3 LocalCoordinatesSite::getYWeights() const { if (yWeights.size() != 3) throw OpenMMException("LocalCoordinatesSite: This version of getYWeights() requires the site to depend on three particles"); return Vec3(yWeights[0], yWeights[1], yWeights[2]); } const Vec3& LocalCoordinatesSite::getLocalPosition() const { return localPosition; } SymmetrySite::SymmetrySite(int particle, const Vec3& Rx, const Vec3& Ry, const Vec3& Rz, const Vec3& v, bool useBoxVectors) : Rx(Rx), Ry(Ry), Rz(Rz), v(v), useBoxVectors(useBoxVectors) { setParticles({particle}); Vec3 R[] = {Rx, Ry, Rz}; for (int i = 0; i < 3; i++) for (int j = i; j < 3; j++) { double dot = R[i].dot(R[j]); if ((i == j && fabs(dot-1) > 1e-6) || (i != j && fabs(dot) > 1e-6)) throw OpenMMException("SymmetrySite: The rotation matrix must be orthogonal"); } } void SymmetrySite::getRotationMatrix(Vec3& Rx, Vec3& Ry, Vec3& Rz) const { Rx = this->Rx; Ry = this->Ry; Rz = this->Rz; } const Vec3& SymmetrySite::getOffsetVector() const { return v; } bool SymmetrySite::getUseBoxVectors() const { return useBoxVectors; }