/* -------------------------------------------------------------------------- * * 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) 2012-2014 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 "ReferenceVirtualSites.h" #include "openmm/VirtualSite.h" #include using namespace OpenMM; using namespace std; void ReferenceVirtualSites::computePositions(const OpenMM::System& system, vector& atomCoordinates) { for (int i = 0; i < system.getNumParticles(); i++) if (system.isVirtualSite(i)) { if (dynamic_cast(&system.getVirtualSite(i)) != NULL) { // A two particle average. const TwoParticleAverageSite& site = dynamic_cast(system.getVirtualSite(i)); int p1 = site.getParticle(0), p2 = site.getParticle(1); double w1 = site.getWeight(0), w2 = site.getWeight(1); atomCoordinates[i] = atomCoordinates[p1]*w1 + atomCoordinates[p2]*w2; } else if (dynamic_cast(&system.getVirtualSite(i)) != NULL) { // A three particle average. const ThreeParticleAverageSite& site = dynamic_cast(system.getVirtualSite(i)); int p1 = site.getParticle(0), p2 = site.getParticle(1), p3 = site.getParticle(2); double w1 = site.getWeight(0), w2 = site.getWeight(1), w3 = site.getWeight(2); atomCoordinates[i] = atomCoordinates[p1]*w1 + atomCoordinates[p2]*w2 + atomCoordinates[p3]*w3; } else if (dynamic_cast(&system.getVirtualSite(i)) != NULL) { // An out of plane site. const OutOfPlaneSite& site = dynamic_cast(system.getVirtualSite(i)); int p1 = site.getParticle(0), p2 = site.getParticle(1), p3 = site.getParticle(2); double w12 = site.getWeight12(), w13 = site.getWeight13(), wcross = site.getWeightCross(); Vec3 v12 = atomCoordinates[p2]-atomCoordinates[p1]; Vec3 v13 = atomCoordinates[p3]-atomCoordinates[p1]; Vec3 cross = v12.cross(v13); atomCoordinates[i] = atomCoordinates[p1] + v12*w12 + v13*w13 + cross*wcross; } else if (dynamic_cast(&system.getVirtualSite(i)) != NULL) { // A local coordinates site. const LocalCoordinatesSite& site = dynamic_cast(system.getVirtualSite(i)); int p1 = site.getParticle(0), p2 = site.getParticle(1), p3 = site.getParticle(2); Vec3 originWeights = site.getOriginWeights(); Vec3 xWeights = site.getXWeights(); Vec3 yWeights = site.getYWeights(); Vec3 localPosition = site.getLocalPosition(); Vec3 origin = atomCoordinates[p1]*originWeights[0] + atomCoordinates[p2]*originWeights[1] + atomCoordinates[p3]*originWeights[2]; Vec3 xdir = atomCoordinates[p1]*xWeights[0] + atomCoordinates[p2]*xWeights[1] + atomCoordinates[p3]*xWeights[2]; Vec3 ydir = atomCoordinates[p1]*yWeights[0] + atomCoordinates[p2]*yWeights[1] + atomCoordinates[p3]*yWeights[2]; Vec3 zdir = xdir.cross(ydir); xdir /= sqrt(xdir.dot(xdir)); zdir /= sqrt(zdir.dot(zdir)); ydir = zdir.cross(xdir); atomCoordinates[i] = origin + xdir*localPosition[0] + ydir*localPosition[1] + zdir*localPosition[2]; } } } void ReferenceVirtualSites::distributeForces(const OpenMM::System& system, const vector& atomCoordinates, vector& forces) { for (int i = 0; i < system.getNumParticles(); i++) if (system.isVirtualSite(i)) { Vec3 f = forces[i]; if (dynamic_cast(&system.getVirtualSite(i)) != NULL) { // A two particle average. const TwoParticleAverageSite& site = dynamic_cast(system.getVirtualSite(i)); int p1 = site.getParticle(0), p2 = site.getParticle(1); double w1 = site.getWeight(0), w2 = site.getWeight(1); forces[p1] += f*w1; forces[p2] += f*w2; } else if (dynamic_cast(&system.getVirtualSite(i)) != NULL) { // A three particle average. const ThreeParticleAverageSite& site = dynamic_cast(system.getVirtualSite(i)); int p1 = site.getParticle(0), p2 = site.getParticle(1), p3 = site.getParticle(2); double w1 = site.getWeight(0), w2 = site.getWeight(1), w3 = site.getWeight(2); forces[p1] += f*w1; forces[p2] += f*w2; forces[p3] += f*w3; } else if (dynamic_cast(&system.getVirtualSite(i)) != NULL) { // An out of plane site. const OutOfPlaneSite& site = dynamic_cast(system.getVirtualSite(i)); int p1 = site.getParticle(0), p2 = site.getParticle(1), p3 = site.getParticle(2); double w12 = site.getWeight12(), w13 = site.getWeight13(), wcross = site.getWeightCross(); Vec3 v12 = atomCoordinates[p2]-atomCoordinates[p1]; Vec3 v13 = atomCoordinates[p3]-atomCoordinates[p1]; Vec3 f2(w12*f[0] - wcross*v13[2]*f[1] + wcross*v13[1]*f[2], wcross*v13[2]*f[0] + w12*f[1] - wcross*v13[0]*f[2], -wcross*v13[1]*f[0] + wcross*v13[0]*f[1] + w12*f[2]); Vec3 f3(w13*f[0] + wcross*v12[2]*f[1] - wcross*v12[1]*f[2], -wcross*v12[2]*f[0] + w13*f[1] + wcross*v12[0]*f[2], wcross*v12[1]*f[0] - wcross*v12[0]*f[1] + w13*f[2]); forces[p1] += f-f2-f3; forces[p2] += f2; forces[p3] += f3; } else if (dynamic_cast(&system.getVirtualSite(i)) != NULL) { // A local coordinates site. const LocalCoordinatesSite& site = dynamic_cast(system.getVirtualSite(i)); int p1 = site.getParticle(0), p2 = site.getParticle(1), p3 = site.getParticle(2); Vec3 originWeights = site.getOriginWeights(); Vec3 wx = site.getXWeights(); Vec3 wy = site.getYWeights(); Vec3 localPosition = site.getLocalPosition(); Vec3 xdir = atomCoordinates[p1]*wx[0] + atomCoordinates[p2]*wx[1] + atomCoordinates[p3]*wx[2]; Vec3 ydir = atomCoordinates[p1]*wy[0] + atomCoordinates[p2]*wy[1] + atomCoordinates[p3]*wy[2]; Vec3 zdir = xdir.cross(ydir); double invNormXdir = 1.0/sqrt(xdir.dot(xdir)); double invNormZdir = 1.0/sqrt(zdir.dot(zdir)); Vec3 dx = xdir*invNormXdir; Vec3 dz = zdir*invNormZdir; Vec3 dy = dz.cross(dx); // The derivatives for this case are very complicated. They were computed with SymPy then simplified by hand. double t11 = (wx[0]*ydir[0]-wy[0]*xdir[0])*invNormZdir; double t12 = (wx[0]*ydir[1]-wy[0]*xdir[1])*invNormZdir; double t13 = (wx[0]*ydir[2]-wy[0]*xdir[2])*invNormZdir; double t21 = (wx[1]*ydir[0]-wy[1]*xdir[0])*invNormZdir; double t22 = (wx[1]*ydir[1]-wy[1]*xdir[1])*invNormZdir; double t23 = (wx[1]*ydir[2]-wy[1]*xdir[2])*invNormZdir; double t31 = (wx[2]*ydir[0]-wy[2]*xdir[0])*invNormZdir; double t32 = (wx[2]*ydir[1]-wy[2]*xdir[1])*invNormZdir; double t33 = (wx[2]*ydir[2]-wy[2]*xdir[2])*invNormZdir; double sx1 = t13*dz[1]-t12*dz[2]; double sy1 = t11*dz[2]-t13*dz[0]; double sz1 = t12*dz[0]-t11*dz[1]; double sx2 = t23*dz[1]-t22*dz[2]; double sy2 = t21*dz[2]-t23*dz[0]; double sz2 = t22*dz[0]-t21*dz[1]; double sx3 = t33*dz[1]-t32*dz[2]; double sy3 = t31*dz[2]-t33*dz[0]; double sz3 = t32*dz[0]-t31*dz[1]; Vec3 wxScaled = wx*invNormXdir; Vec3 fp1 = localPosition*f[0]; Vec3 fp2 = localPosition*f[1]; Vec3 fp3 = localPosition*f[2]; forces[p1][0] += fp1[0]*wxScaled[0]*(1-dx[0]*dx[0]) + fp1[2]*(dz[0]*sx1 ) + fp1[1]*((-dx[0]*dy[0] )*wxScaled[0] + dy[0]*sx1 - dx[1]*t12 - dx[2]*t13) + f[0]*originWeights[0]; forces[p1][1] += fp1[0]*wxScaled[0]*( -dx[0]*dx[1]) + fp1[2]*(dz[0]*sy1+t13) + fp1[1]*((-dx[1]*dy[0]-dz[2])*wxScaled[0] + dy[0]*sy1 + dx[1]*t11); forces[p1][2] += fp1[0]*wxScaled[0]*( -dx[0]*dx[2]) + fp1[2]*(dz[0]*sz1-t12) + fp1[1]*((-dx[2]*dy[0]+dz[1])*wxScaled[0] + dy[0]*sz1 + dx[2]*t11); forces[p2][0] += fp1[0]*wxScaled[1]*(1-dx[0]*dx[0]) + fp1[2]*(dz[0]*sx2 ) + fp1[1]*((-dx[0]*dy[0] )*wxScaled[1] + dy[0]*sx2 - dx[1]*t22 - dx[2]*t23) + f[0]*originWeights[1]; forces[p2][1] += fp1[0]*wxScaled[1]*( -dx[0]*dx[1]) + fp1[2]*(dz[0]*sy2+t23) + fp1[1]*((-dx[1]*dy[0]-dz[2])*wxScaled[1] + dy[0]*sy2 + dx[1]*t21); forces[p2][2] += fp1[0]*wxScaled[1]*( -dx[0]*dx[2]) + fp1[2]*(dz[0]*sz2-t22) + fp1[1]*((-dx[2]*dy[0]+dz[1])*wxScaled[1] + dy[0]*sz2 + dx[2]*t21); forces[p3][0] += fp1[0]*wxScaled[2]*(1-dx[0]*dx[0]) + fp1[2]*(dz[0]*sx3 ) + fp1[1]*((-dx[0]*dy[0] )*wxScaled[2] + dy[0]*sx3 - dx[1]*t32 - dx[2]*t33) + f[0]*originWeights[2]; forces[p3][1] += fp1[0]*wxScaled[2]*( -dx[0]*dx[1]) + fp1[2]*(dz[0]*sy3+t33) + fp1[1]*((-dx[1]*dy[0]-dz[2])*wxScaled[2] + dy[0]*sy3 + dx[1]*t31); forces[p3][2] += fp1[0]*wxScaled[2]*( -dx[0]*dx[2]) + fp1[2]*(dz[0]*sz3-t32) + fp1[1]*((-dx[2]*dy[0]+dz[1])*wxScaled[2] + dy[0]*sz3 + dx[2]*t31); forces[p1][0] += fp2[0]*wxScaled[0]*( -dx[1]*dx[0]) + fp2[2]*(dz[1]*sx1-t13) - fp2[1]*(( dx[0]*dy[1]-dz[2])*wxScaled[0] - dy[1]*sx1 - dx[0]*t12); forces[p1][1] += fp2[0]*wxScaled[0]*(1-dx[1]*dx[1]) + fp2[2]*(dz[1]*sy1 ) - fp2[1]*(( dx[1]*dy[1] )*wxScaled[0] - dy[1]*sy1 + dx[0]*t11 + dx[2]*t13) + f[1]*originWeights[0]; forces[p1][2] += fp2[0]*wxScaled[0]*( -dx[1]*dx[2]) + fp2[2]*(dz[1]*sz1+t11) - fp2[1]*(( dx[2]*dy[1]+dz[0])*wxScaled[0] - dy[1]*sz1 - dx[2]*t12); forces[p2][0] += fp2[0]*wxScaled[1]*( -dx[1]*dx[0]) + fp2[2]*(dz[1]*sx2-t23) - fp2[1]*(( dx[0]*dy[1]-dz[2])*wxScaled[1] - dy[1]*sx2 - dx[0]*t22); forces[p2][1] += fp2[0]*wxScaled[1]*(1-dx[1]*dx[1]) + fp2[2]*(dz[1]*sy2 ) - fp2[1]*(( dx[1]*dy[1] )*wxScaled[1] - dy[1]*sy2 + dx[0]*t21 + dx[2]*t23) + f[1]*originWeights[1]; forces[p2][2] += fp2[0]*wxScaled[1]*( -dx[1]*dx[2]) + fp2[2]*(dz[1]*sz2+t21) - fp2[1]*(( dx[2]*dy[1]+dz[0])*wxScaled[1] - dy[1]*sz2 - dx[2]*t22); forces[p3][0] += fp2[0]*wxScaled[2]*( -dx[1]*dx[0]) + fp2[2]*(dz[1]*sx3-t33) - fp2[1]*(( dx[0]*dy[1]-dz[2])*wxScaled[2] - dy[1]*sx3 - dx[0]*t32); forces[p3][1] += fp2[0]*wxScaled[2]*(1-dx[1]*dx[1]) + fp2[2]*(dz[1]*sy3 ) - fp2[1]*(( dx[1]*dy[1] )*wxScaled[2] - dy[1]*sy3 + dx[0]*t31 + dx[2]*t33) + f[1]*originWeights[2]; forces[p3][2] += fp2[0]*wxScaled[2]*( -dx[1]*dx[2]) + fp2[2]*(dz[1]*sz3+t31) - fp2[1]*(( dx[2]*dy[1]+dz[0])*wxScaled[2] - dy[1]*sz3 - dx[2]*t32); forces[p1][0] += fp3[0]*wxScaled[0]*( -dx[2]*dx[0]) + fp3[2]*(dz[2]*sx1+t12) + fp3[1]*((-dx[0]*dy[2]-dz[1])*wxScaled[0] + dy[2]*sx1 + dx[0]*t13); forces[p1][1] += fp3[0]*wxScaled[0]*( -dx[2]*dx[1]) + fp3[2]*(dz[2]*sy1-t11) + fp3[1]*((-dx[1]*dy[2]+dz[0])*wxScaled[0] + dy[2]*sy1 + dx[1]*t13); forces[p1][2] += fp3[0]*wxScaled[0]*(1-dx[2]*dx[2]) + fp3[2]*(dz[2]*sz1 ) + fp3[1]*((-dx[2]*dy[2] )*wxScaled[0] + dy[2]*sz1 - dx[0]*t11 - dx[1]*t12) + f[2]*originWeights[0]; forces[p2][0] += fp3[0]*wxScaled[1]*( -dx[2]*dx[0]) + fp3[2]*(dz[2]*sx2+t22) + fp3[1]*((-dx[0]*dy[2]-dz[1])*wxScaled[1] + dy[2]*sx2 + dx[0]*t23); forces[p2][1] += fp3[0]*wxScaled[1]*( -dx[2]*dx[1]) + fp3[2]*(dz[2]*sy2-t21) + fp3[1]*((-dx[1]*dy[2]+dz[0])*wxScaled[1] + dy[2]*sy2 + dx[1]*t23); forces[p2][2] += fp3[0]*wxScaled[1]*(1-dx[2]*dx[2]) + fp3[2]*(dz[2]*sz2 ) + fp3[1]*((-dx[2]*dy[2] )*wxScaled[1] + dy[2]*sz2 - dx[0]*t21 - dx[1]*t22) + f[2]*originWeights[1]; forces[p3][0] += fp3[0]*wxScaled[2]*( -dx[2]*dx[0]) + fp3[2]*(dz[2]*sx3+t32) + fp3[1]*((-dx[0]*dy[2]-dz[1])*wxScaled[2] + dy[2]*sx3 + dx[0]*t33); forces[p3][1] += fp3[0]*wxScaled[2]*( -dx[2]*dx[1]) + fp3[2]*(dz[2]*sy3-t31) + fp3[1]*((-dx[1]*dy[2]+dz[0])*wxScaled[2] + dy[2]*sy3 + dx[1]*t33); forces[p3][2] += fp3[0]*wxScaled[2]*(1-dx[2]*dx[2]) + fp3[2]*(dz[2]*sz3 ) + fp3[1]*((-dx[2]*dy[2] )*wxScaled[2] + dy[2]*sz3 - dx[0]*t31 - dx[1]*t32) + f[2]*originWeights[2]; } } }