ReferenceVirtualSites.cpp

/* -------------------------------------------------------------------------- *
 *                                   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) 2012-2025 Stanford University and the Authors.      *
 * Authors: Peter Eastman                                                     *
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#include "ReferenceVirtualSites.h"
#include "openmm/VirtualSite.h"
#include "openmm/OpenMMException.h"
#include <cmath>
#include <set>

using namespace OpenMM;
using namespace std;

ReferenceVirtualSites::ReferenceVirtualSites(const System& system) {
    set<int> sites;
    for (int i = 0; i < system.getNumParticles(); i++)
        if (system.isVirtualSite(i))
            sites.insert(i);
    int remainingSites = 0;
    while (sites.size() > 0) {
        if (sites.size() == remainingSites)
            throw OpenMMException("Virtual site definitions are circular");
        remainingSites = sites.size();
        for (auto index = sites.begin(); index != sites.end();) {
            const VirtualSite& site = system.getVirtualSite(*index);
            bool canCompute = true;
            for (int i = 0; i < site.getNumParticles(); i++)
                if (sites.find(site.getParticle(i)) != sites.end())
                    canCompute = false;
            if (canCompute) {
                order.push_back(*index);
                index = sites.erase(index);
            }
            else
                ++index;
        }
    }
}

void ReferenceVirtualSites::computePositions(const OpenMM::System& system, vector<OpenMM::Vec3>& atomCoordinates) const {
    for (int i : order) {
        if (dynamic_cast<const TwoParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) {
            // A two particle average.

            const TwoParticleAverageSite& site = dynamic_cast<const TwoParticleAverageSite&>(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<const ThreeParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) {
            // A three particle average.

            const ThreeParticleAverageSite& site = dynamic_cast<const ThreeParticleAverageSite&>(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<const OutOfPlaneSite*>(&system.getVirtualSite(i)) != NULL) {
            // An out of plane site.

            const OutOfPlaneSite& site = dynamic_cast<const OutOfPlaneSite&>(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<const LocalCoordinatesSite*>(&system.getVirtualSite(i)) != NULL) {
            // A local coordinates site.

            const LocalCoordinatesSite& site = dynamic_cast<const LocalCoordinatesSite&>(system.getVirtualSite(i));
            int numParticles = site.getNumParticles();
            vector<double> originWeights, xWeights, yWeights;
            site.getOriginWeights(originWeights);
            site.getXWeights(xWeights);
            site.getYWeights(yWeights);
            Vec3 origin, xdir, ydir;
            for (int j = 0; j < numParticles; j++) {
                Vec3 pos = atomCoordinates[site.getParticle(j)];
                origin += pos*originWeights[j];
                xdir += pos*xWeights[j];
                ydir += pos*yWeights[j];
            }
            Vec3 localPosition = site.getLocalPosition();
            Vec3 zdir = xdir.cross(ydir);
            double normXdir = sqrt(xdir.dot(xdir));
            double normZdir = sqrt(zdir.dot(zdir));
            if (normXdir > 0.0)
                xdir /= normXdir;
            if (normZdir > 0.0)
                zdir /= normZdir;
            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<OpenMM::Vec3>& atomCoordinates, vector<OpenMM::Vec3>& forces) const {
    for (auto iter = order.rbegin(); iter != order.rend(); ++iter) {
        int i = *iter;
        Vec3 f = forces[i];
        if (dynamic_cast<const TwoParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) {
            // A two particle average.

            const TwoParticleAverageSite& site = dynamic_cast<const TwoParticleAverageSite&>(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<const ThreeParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) {
            // A three particle average.

            const ThreeParticleAverageSite& site = dynamic_cast<const ThreeParticleAverageSite&>(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<const OutOfPlaneSite*>(&system.getVirtualSite(i)) != NULL) {
            // An out of plane site.

            const OutOfPlaneSite& site = dynamic_cast<const OutOfPlaneSite&>(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<const LocalCoordinatesSite*>(&system.getVirtualSite(i)) != NULL) {
            // A local coordinates site.

            const LocalCoordinatesSite& site = dynamic_cast<const LocalCoordinatesSite&>(system.getVirtualSite(i));
            int numParticles = site.getNumParticles();
            vector<double> originWeights, wx, wy;
            site.getOriginWeights(originWeights);
            site.getXWeights(wx);
            site.getYWeights(wy);
            Vec3 xdir, ydir;
            for (int j = 0; j < numParticles; j++) {
                Vec3 pos = atomCoordinates[site.getParticle(j)];
                xdir += pos*wx[j];
                ydir += pos*wy[j];
            }
            Vec3 localPosition = site.getLocalPosition();
            Vec3 zdir = xdir.cross(ydir);
            double normXdir = sqrt(xdir.dot(xdir));
            double normZdir = sqrt(zdir.dot(zdir));
            double invNormXdir = (normXdir > 0.0 ? 1.0/normXdir : 0.0);
            double invNormZdir = (normZdir > 0.0 ? 1.0/normZdir : 0.0);
            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.

            vector<double> wxScaled(numParticles);
            for (int j = 0; j < numParticles; j++)
                wxScaled[j] = wx[j]*invNormXdir;
            Vec3 fp1 = localPosition*f[0];
            Vec3 fp2 = localPosition*f[1];
            Vec3 fp3 = localPosition*f[2];
            for (int j = 0; j < numParticles; j++) {
                double t1 = (wx[j]*ydir[0]-wy[j]*xdir[0])*invNormZdir;
                double t2 = (wx[j]*ydir[1]-wy[j]*xdir[1])*invNormZdir;
                double t3 = (wx[j]*ydir[2]-wy[j]*xdir[2])*invNormZdir;
                double sx = t3*dz[1]-t2*dz[2];
                double sy = t1*dz[2]-t3*dz[0];
                double sz = t2*dz[0]-t1*dz[1];
                int p = site.getParticle(j);
                forces[p][0] += fp1[0]*wxScaled[j]*(1-dx[0]*dx[0]) + fp1[2]*(dz[0]*sx   ) + fp1[1]*((-dx[0]*dy[0]      )*wxScaled[j] + dy[0]*sx - dx[1]*t2 - dx[2]*t3) + f[0]*originWeights[j];
                forces[p][1] += fp1[0]*wxScaled[j]*( -dx[0]*dx[1]) + fp1[2]*(dz[0]*sy+t3) + fp1[1]*((-dx[1]*dy[0]-dz[2])*wxScaled[j] + dy[0]*sy + dx[1]*t1);
                forces[p][2] += fp1[0]*wxScaled[j]*( -dx[0]*dx[2]) + fp1[2]*(dz[0]*sz-t2) + fp1[1]*((-dx[2]*dy[0]+dz[1])*wxScaled[j] + dy[0]*sz + dx[2]*t1);
                forces[p][0] += fp2[0]*wxScaled[j]*( -dx[1]*dx[0]) + fp2[2]*(dz[1]*sx-t3) - fp2[1]*(( dx[0]*dy[1]-dz[2])*wxScaled[j] - dy[1]*sx - dx[0]*t2);
                forces[p][1] += fp2[0]*wxScaled[j]*(1-dx[1]*dx[1]) + fp2[2]*(dz[1]*sy   ) - fp2[1]*(( dx[1]*dy[1]      )*wxScaled[j] - dy[1]*sy + dx[0]*t1 + dx[2]*t3) + f[1]*originWeights[j];
                forces[p][2] += fp2[0]*wxScaled[j]*( -dx[1]*dx[2]) + fp2[2]*(dz[1]*sz+t1) - fp2[1]*(( dx[2]*dy[1]+dz[0])*wxScaled[j] - dy[1]*sz - dx[2]*t2);
                forces[p][0] += fp3[0]*wxScaled[j]*( -dx[2]*dx[0]) + fp3[2]*(dz[2]*sx+t2) + fp3[1]*((-dx[0]*dy[2]-dz[1])*wxScaled[j] + dy[2]*sx + dx[0]*t3);
                forces[p][1] += fp3[0]*wxScaled[j]*( -dx[2]*dx[1]) + fp3[2]*(dz[2]*sy-t1) + fp3[1]*((-dx[1]*dy[2]+dz[0])*wxScaled[j] + dy[2]*sy + dx[1]*t3);
                forces[p][2] += fp3[0]*wxScaled[j]*(1-dx[2]*dx[2]) + fp3[2]*(dz[2]*sz   ) + fp3[1]*((-dx[2]*dy[2]      )*wxScaled[j] + dy[2]*sz - dx[0]*t1 - dx[1]*t2) + f[2]*originWeights[j];
            }
       }
    }
}