/* -------------------------------------------------------------------------- * * 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) 2013 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 "ReferenceSETTLEAlgorithm.h" using namespace OpenMM; using namespace std; ReferenceSETTLEAlgorithm::ReferenceSETTLEAlgorithm(const vector& atom1, const vector& atom2, const vector& atom3, const vector& distance1, const vector& distance2, vector& masses) : atom1(atom1), atom2(atom2), atom3(atom3), distance1(distance1), distance2(distance2), masses(masses) { } int ReferenceSETTLEAlgorithm::getNumClusters() const { return atom1.size(); } void ReferenceSETTLEAlgorithm::getClusterParameters(int index, int& atom1, int& atom2, int& atom3, double& distance1, double& distance2) const { atom1 = this->atom1[index]; atom2 = this->atom2[index]; atom3 = this->atom3[index]; distance1 = this->distance1[index]; distance2 = this->distance2[index]; } void ReferenceSETTLEAlgorithm::apply(vector& atomCoordinates, vector& atomCoordinatesP, vector& inverseMasses, double tolerance) { for (int index = 0; index < (int) atom1.size(); ++index) { Vec3 apos0 = atomCoordinates[atom1[index]]; Vec3 xp0 = atomCoordinatesP[atom1[index]]-apos0; Vec3 apos1 = atomCoordinates[atom2[index]]; Vec3 xp1 = atomCoordinatesP[atom2[index]]-apos1; Vec3 apos2 = atomCoordinates[atom3[index]]; Vec3 xp2 = atomCoordinatesP[atom3[index]]-apos2; double m0 = masses[atom1[index]]; double m1 = masses[atom2[index]]; double m2 = masses[atom3[index]]; // Apply the SETTLE algorithm. double xb0 = apos1[0]-apos0[0]; double yb0 = apos1[1]-apos0[1]; double zb0 = apos1[2]-apos0[2]; double xc0 = apos2[0]-apos0[0]; double yc0 = apos2[1]-apos0[1]; double zc0 = apos2[2]-apos0[2]; double invTotalMass = 1/(m0+m1+m2); double xcom = (xp0[0]*m0 + (xb0+xp1[0])*m1 + (xc0+xp2[0])*m2) * invTotalMass; double ycom = (xp0[1]*m0 + (yb0+xp1[1])*m1 + (yc0+xp2[1])*m2) * invTotalMass; double zcom = (xp0[2]*m0 + (zb0+xp1[2])*m1 + (zc0+xp2[2])*m2) * invTotalMass; double xa1 = xp0[0] - xcom; double ya1 = xp0[1] - ycom; double za1 = xp0[2] - zcom; double xb1 = xb0 + xp1[0] - xcom; double yb1 = yb0 + xp1[1] - ycom; double zb1 = zb0 + xp1[2] - zcom; double xc1 = xc0 + xp2[0] - xcom; double yc1 = yc0 + xp2[1] - ycom; double zc1 = zc0 + xp2[2] - zcom; double xaksZd = yb0*zc0 - zb0*yc0; double yaksZd = zb0*xc0 - xb0*zc0; double zaksZd = xb0*yc0 - yb0*xc0; double xaksXd = ya1*zaksZd - za1*yaksZd; double yaksXd = za1*xaksZd - xa1*zaksZd; double zaksXd = xa1*yaksZd - ya1*xaksZd; double xaksYd = yaksZd*zaksXd - zaksZd*yaksXd; double yaksYd = zaksZd*xaksXd - xaksZd*zaksXd; double zaksYd = xaksZd*yaksXd - yaksZd*xaksXd; double axlng = sqrt(xaksXd*xaksXd + yaksXd*yaksXd + zaksXd*zaksXd); double aylng = sqrt(xaksYd*xaksYd + yaksYd*yaksYd + zaksYd*zaksYd); double azlng = sqrt(xaksZd*xaksZd + yaksZd*yaksZd + zaksZd*zaksZd); double trns11 = xaksXd / axlng; double trns21 = yaksXd / axlng; double trns31 = zaksXd / axlng; double trns12 = xaksYd / aylng; double trns22 = yaksYd / aylng; double trns32 = zaksYd / aylng; double trns13 = xaksZd / azlng; double trns23 = yaksZd / azlng; double trns33 = zaksZd / azlng; double xb0d = trns11*xb0 + trns21*yb0 + trns31*zb0; double yb0d = trns12*xb0 + trns22*yb0 + trns32*zb0; double xc0d = trns11*xc0 + trns21*yc0 + trns31*zc0; double yc0d = trns12*xc0 + trns22*yc0 + trns32*zc0; double za1d = trns13*xa1 + trns23*ya1 + trns33*za1; double xb1d = trns11*xb1 + trns21*yb1 + trns31*zb1; double yb1d = trns12*xb1 + trns22*yb1 + trns32*zb1; double zb1d = trns13*xb1 + trns23*yb1 + trns33*zb1; double xc1d = trns11*xc1 + trns21*yc1 + trns31*zc1; double yc1d = trns12*xc1 + trns22*yc1 + trns32*zc1; double zc1d = trns13*xc1 + trns23*yc1 + trns33*zc1; // --- Step2 A2' --- double rc = 0.5*distance2[index]; double rb = sqrt(distance1[index]*distance1[index]-rc*rc); double ra = rb*(m1+m2)*invTotalMass; rb -= ra; double sinphi = za1d / ra; double cosphi = sqrt(1 - sinphi*sinphi); double sinpsi = (zb1d - zc1d) / (2*rc*cosphi); double cospsi = sqrt(1 - sinpsi*sinpsi); double ya2d = ra*cosphi; double xb2d = - rc*cospsi; double yb2d = - rb*cosphi - rc*sinpsi*sinphi; double yc2d = - rb*cosphi + rc*sinpsi*sinphi; double xb2d2 = xb2d*xb2d; double hh2 = 4.0f*xb2d2 + (yb2d-yc2d)*(yb2d-yc2d) + (zb1d-zc1d)*(zb1d-zc1d); double deltx = 2.0f*xb2d + sqrt(4.0f*xb2d2 - hh2 + distance2[index]*distance2[index]); xb2d -= deltx*0.5; // --- Step3 al,be,ga --- double alpha = (xb2d*(xb0d-xc0d) + yb0d*yb2d + yc0d*yc2d); double beta = (xb2d*(yc0d-yb0d) + xb0d*yb2d + xc0d*yc2d); double gamma = xb0d*yb1d - xb1d*yb0d + xc0d*yc1d - xc1d*yc0d; double al2be2 = alpha*alpha + beta*beta; double sintheta = (alpha*gamma - beta*sqrt(al2be2 - gamma*gamma)) / al2be2; // --- Step4 A3' --- double costheta = sqrt(1 - sintheta*sintheta); double xa3d = - ya2d*sintheta; double ya3d = ya2d*costheta; double za3d = za1d; double xb3d = xb2d*costheta - yb2d*sintheta; double yb3d = xb2d*sintheta + yb2d*costheta; double zb3d = zb1d; double xc3d = - xb2d*costheta - yc2d*sintheta; double yc3d = - xb2d*sintheta + yc2d*costheta; double zc3d = zc1d; // --- Step5 A3 --- double xa3 = trns11*xa3d + trns12*ya3d + trns13*za3d; double ya3 = trns21*xa3d + trns22*ya3d + trns23*za3d; double za3 = trns31*xa3d + trns32*ya3d + trns33*za3d; double xb3 = trns11*xb3d + trns12*yb3d + trns13*zb3d; double yb3 = trns21*xb3d + trns22*yb3d + trns23*zb3d; double zb3 = trns31*xb3d + trns32*yb3d + trns33*zb3d; double xc3 = trns11*xc3d + trns12*yc3d + trns13*zc3d; double yc3 = trns21*xc3d + trns22*yc3d + trns23*zc3d; double zc3 = trns31*xc3d + trns32*yc3d + trns33*zc3d; xp0[0] = xcom + xa3; xp0[1] = ycom + ya3; xp0[2] = zcom + za3; xp1[0] = xcom + xb3 - xb0; xp1[1] = ycom + yb3 - yb0; xp1[2] = zcom + zb3 - zb0; xp2[0] = xcom + xc3 - xc0; xp2[1] = ycom + yc3 - yc0; xp2[2] = zcom + zc3 - zc0; // Record the new positions. atomCoordinatesP[atom1[index]] = xp0+apos0; atomCoordinatesP[atom2[index]] = xp1+apos1; atomCoordinatesP[atom3[index]] = xp2+apos2; } } void ReferenceSETTLEAlgorithm::applyToVelocities(vector& atomCoordinates, vector& velocities, vector& inverseMasses, double tolerance) { for (int index = 0; index < (int) atom1.size(); ++index) { Vec3 apos0 = atomCoordinates[atom1[index]]; Vec3 apos1 = atomCoordinates[atom2[index]]; Vec3 apos2 = atomCoordinates[atom3[index]]; Vec3 v0 = velocities[atom1[index]]; Vec3 v1 = velocities[atom2[index]]; Vec3 v2 = velocities[atom3[index]]; // Compute intermediate quantities: the atom masses, the bond directions, the relative velocities, // and the angle cosines and sines. double mA = masses[atom1[index]]; double mB = masses[atom2[index]]; double mC = masses[atom3[index]]; Vec3 eAB = apos1-apos0; Vec3 eBC = apos2-apos1; Vec3 eCA = apos0-apos2; eAB /= sqrt(eAB[0]*eAB[0] + eAB[1]*eAB[1] + eAB[2]*eAB[2]); eBC /= sqrt(eBC[0]*eBC[0] + eBC[1]*eBC[1] + eBC[2]*eBC[2]); eCA /= sqrt(eCA[0]*eCA[0] + eCA[1]*eCA[1] + eCA[2]*eCA[2]); double vAB = (v1[0]-v0[0])*eAB[0] + (v1[1]-v0[1])*eAB[1] + (v1[2]-v0[2])*eAB[2]; double vBC = (v2[0]-v1[0])*eBC[0] + (v2[1]-v1[1])*eBC[1] + (v2[2]-v1[2])*eBC[2]; double vCA = (v0[0]-v2[0])*eCA[0] + (v0[1]-v2[1])*eCA[1] + (v0[2]-v2[2])*eCA[2]; double cA = -(eAB[0]*eCA[0] + eAB[1]*eCA[1] + eAB[2]*eCA[2]); double cB = -(eAB[0]*eBC[0] + eAB[1]*eBC[1] + eAB[2]*eBC[2]); double cC = -(eBC[0]*eCA[0] + eBC[1]*eCA[1] + eBC[2]*eCA[2]); double s2A = 1-cA*cA; double s2B = 1-cB*cB; double s2C = 1-cC*cC; // Solve the equations. These are different from those in the SETTLE paper (JCC 13(8), pp. 952-962, 1992), because // in going from equations B1 to B2, they make the assumption that mB=mC (but don't bother to mention they're // making that assumption). We allow all three atoms to have different masses. double mABCinv = 1/(mA*mB*mC); double denom = (((s2A*mB+s2B*mA)*mC+(s2A*mB*mB+2*(cA*cB*cC+1)*mA*mB+s2B*mA*mA))*mC+s2C*mA*mB*(mA+mB))*mABCinv; double tab = ((cB*cC*mA-cA*mB-cA*mC)*vCA + (cA*cC*mB-cB*mC-cB*mA)*vBC + (s2C*mA*mA*mB*mB*mABCinv+(mA+mB+mC))*vAB)/denom; double tbc = ((cA*cB*mC-cC*mB-cC*mA)*vCA + (s2A*mB*mB*mC*mC*mABCinv+(mA+mB+mC))*vBC + (cA*cC*mB-cB*mA-cB*mC)*vAB)/denom; double tca = ((s2B*mA*mA*mC*mC*mABCinv+(mA+mB+mC))*vCA + (cA*cB*mC-cC*mB-cC*mA)*vBC + (cB*cC*mA-cA*mB-cA*mC)*vAB)/denom; v0 += (eAB*tab - eCA*tca)*inverseMasses[atom1[index]]; v1 += (eBC*tbc - eAB*tab)*inverseMasses[atom2[index]]; v2 += (eCA*tca - eBC*tbc)*inverseMasses[atom3[index]]; velocities[atom1[index]] = v0; velocities[atom2[index]] = v1; velocities[atom3[index]] = v2; } }