CpuNonbondedForceVec4.cpp

/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
 * Contributors: Pande Group
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#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "CpuNonbondedForceVec4.h"

using namespace std;
using namespace OpenMM;

/**
 * Factory method to create a CpuNonbondedForceVec4.
 */
CpuNonbondedForce* createCpuNonbondedForceVec4() {
    return new CpuNonbondedForceVec4();
}

/**---------------------------------------------------------------------------------------

   CpuNonbondedForceVec4 constructor

   --------------------------------------------------------------------------------------- */

CpuNonbondedForceVec4::CpuNonbondedForceVec4() {
}

void CpuNonbondedForceVec4::calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
    // Load the positions and parameters of the atoms in the block.
    
    int blockAtom[4];
    fvec4 blockAtomPosq[4];
    fvec4 blockAtomForceX(0.0f), blockAtomForceY(0.0f), blockAtomForceZ(0.0f);
    for (int i = 0; i < 4; i++) {
        blockAtom[i] = neighborList->getSortedAtoms()[4*blockIndex+i];
        blockAtomPosq[i] = fvec4(posq+4*blockAtom[i]);
    }
    fvec4 blockAtomX = fvec4(blockAtomPosq[0][0], blockAtomPosq[1][0], blockAtomPosq[2][0], blockAtomPosq[3][0]);
    fvec4 blockAtomY = fvec4(blockAtomPosq[0][1], blockAtomPosq[1][1], blockAtomPosq[2][1], blockAtomPosq[3][1]);
    fvec4 blockAtomZ = fvec4(blockAtomPosq[0][2], blockAtomPosq[1][2], blockAtomPosq[2][2], blockAtomPosq[3][2]);
    fvec4 blockAtomCharge = fvec4(ONE_4PI_EPS0)*fvec4(blockAtomPosq[0][3], blockAtomPosq[1][3], blockAtomPosq[2][3], blockAtomPosq[3][3]);
    fvec4 blockAtomSigma(atomParameters[blockAtom[0]].first, atomParameters[blockAtom[1]].first, atomParameters[blockAtom[2]].first, atomParameters[blockAtom[3]].first);
    fvec4 blockAtomEpsilon(atomParameters[blockAtom[0]].second, atomParameters[blockAtom[1]].second, atomParameters[blockAtom[2]].second, atomParameters[blockAtom[3]].second);
    bool needPeriodic = (periodic && (any(blockAtomX < cutoffDistance) || any(blockAtomY < cutoffDistance) || any(blockAtomZ < cutoffDistance) ||
            any(blockAtomX > boxSize[0]-cutoffDistance) || any(blockAtomY > boxSize[1]-cutoffDistance) || any(blockAtomZ > boxSize[2]-cutoffDistance)));
    const float invSwitchingInterval = 1/(cutoffDistance-switchingDistance);
    
    // Loop over neighbors for this block.
    
    const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
    const vector<char>& exclusions = neighborList->getBlockExclusions(blockIndex);
    for (int i = 0; i < (int) neighbors.size(); i++) {
        // Load the next neighbor.
        
        int atom = neighbors[i];
        
        // Compute the distances to the block atoms.
        
        fvec4 dx, dy, dz, r2;
        getDeltaR(posq+4*atom, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
        ivec4 include;
        char excl = exclusions[i];
        if (excl == 0)
            include = -1;
        else
            include = ivec4(excl&1 ? 0 : -1, excl&2 ? 0 : -1, excl&4 ? 0 : -1, excl&8 ? 0 : -1);
        include = include & (r2 < cutoffDistance*cutoffDistance);
        if (!any(include))
            continue; // No interactions to compute.
        
        // Compute the interactions.
        
        fvec4 r = sqrt(r2);
        fvec4 inverseR = fvec4(1.0f)/r;
        fvec4 energy, dEdR;
        float atomEpsilon = atomParameters[atom].second;
        if (atomEpsilon != 0.0f) {
            fvec4 sig = blockAtomSigma+atomParameters[atom].first;
            fvec4 sig2 = inverseR*sig;
            sig2 *= sig2;
            fvec4 sig6 = sig2*sig2*sig2;
            fvec4 epsSig6 = blockAtomEpsilon*atomEpsilon*sig6;
            dEdR = epsSig6*(12.0f*sig6 - 6.0f);
            energy = epsSig6*(sig6-1.0f);
            if (useSwitch) {
                fvec4 t = (r>switchingDistance) & ((r-switchingDistance)*invSwitchingInterval);
                fvec4 switchValue = 1+t*t*t*(-10.0f+t*(15.0f-t*6.0f));
                fvec4 switchDeriv = t*t*(-30.0f+t*(60.0f-t*30.0f))*invSwitchingInterval;
                dEdR = switchValue*dEdR - energy*switchDeriv*r;
                energy *= switchValue;
            }
        }
        else {
            energy = 0.0f;
            dEdR = 0.0f;
        }
        fvec4 chargeProd = blockAtomCharge*posq[4*atom+3];
        if (cutoff)
            dEdR += chargeProd*(inverseR-2.0f*krf*r2);
        else
            dEdR += chargeProd*inverseR;
        dEdR *= inverseR*inverseR;

        // Accumulate energies.

        fvec4 one(1.0f);
        if (totalEnergy) {
            if (cutoff)
                energy += chargeProd*(inverseR+krf*r2-crf);
            else
                energy += chargeProd*inverseR;
            energy = blend(0.0f, energy, include);
            *totalEnergy += dot4(energy, one);
        }

        // Accumulate forces.

        dEdR = blend(0.0f, dEdR, include);
        fvec4 fx = dx*dEdR;
        fvec4 fy = dy*dEdR;
        fvec4 fz = dz*dEdR;
        blockAtomForceX += fx;
        blockAtomForceY += fy;
        blockAtomForceZ += fz;
        float* atomForce = forces+4*atom;
        atomForce[0] -= dot4(fx, one);
        atomForce[1] -= dot4(fy, one);
        atomForce[2] -= dot4(fz, one);
    }
    
    // Record the forces on the block atoms.

    fvec4 f[4] = {blockAtomForceX, blockAtomForceY, blockAtomForceZ, 0.0f};
    transpose(f[0], f[1], f[2], f[3]);
    for (int j = 0; j < 4; j++)
        (fvec4(forces+4*blockAtom[j])+f[j]).store(forces+4*blockAtom[j]);
  }

void CpuNonbondedForceVec4::calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
    // Load the positions and parameters of the atoms in the block.
    
    int blockAtom[4];
    fvec4 blockAtomPosq[4];
    fvec4 blockAtomForceX(0.0f), blockAtomForceY(0.0f), blockAtomForceZ(0.0f);
    for (int i = 0; i < 4; i++) {
        blockAtom[i] = neighborList->getSortedAtoms()[4*blockIndex+i];
        blockAtomPosq[i] = fvec4(posq+4*blockAtom[i]);
    }
    fvec4 blockAtomX = fvec4(blockAtomPosq[0][0], blockAtomPosq[1][0], blockAtomPosq[2][0], blockAtomPosq[3][0]);
    fvec4 blockAtomY = fvec4(blockAtomPosq[0][1], blockAtomPosq[1][1], blockAtomPosq[2][1], blockAtomPosq[3][1]);
    fvec4 blockAtomZ = fvec4(blockAtomPosq[0][2], blockAtomPosq[1][2], blockAtomPosq[2][2], blockAtomPosq[3][2]);
    fvec4 blockAtomCharge = fvec4(ONE_4PI_EPS0)*fvec4(blockAtomPosq[0][3], blockAtomPosq[1][3], blockAtomPosq[2][3], blockAtomPosq[3][3]);
    fvec4 blockAtomSigma(atomParameters[blockAtom[0]].first, atomParameters[blockAtom[1]].first, atomParameters[blockAtom[2]].first, atomParameters[blockAtom[3]].first);
    fvec4 blockAtomEpsilon(atomParameters[blockAtom[0]].second, atomParameters[blockAtom[1]].second, atomParameters[blockAtom[2]].second, atomParameters[blockAtom[3]].second);
    bool needPeriodic = (periodic && (any(blockAtomX < cutoffDistance) || any(blockAtomY < cutoffDistance) || any(blockAtomZ < cutoffDistance) ||
            any(blockAtomX > boxSize[0]-cutoffDistance) || any(blockAtomY > boxSize[1]-cutoffDistance) || any(blockAtomZ > boxSize[2]-cutoffDistance)));
    const float invSwitchingInterval = 1/(cutoffDistance-switchingDistance);
    
    // Loop over neighbors for this block.
    
    const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
    const vector<char>& exclusions = neighborList->getBlockExclusions(blockIndex);
    for (int i = 0; i < (int) neighbors.size(); i++) {
        // Load the next neighbor.
        
        int atom = neighbors[i];
        
        // Compute the distances to the block atoms.
        
        fvec4 dx, dy, dz, r2;
        getDeltaR(posq+4*atom, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
        ivec4 include;
        char excl = exclusions[i];
        if (excl == 0)
            include = -1;
        else
            include = ivec4(excl&1 ? 0 : -1, excl&2 ? 0 : -1, excl&4 ? 0 : -1, excl&8 ? 0 : -1);
        include = include & (r2 < cutoffDistance*cutoffDistance);
        if (!any(include))
            continue; // No interactions to compute.
        
        // Compute the interactions.
        
        fvec4 r = sqrt(r2);
        fvec4 inverseR = fvec4(1.0f)/r;
        fvec4 energy, dEdR;
        float atomEpsilon = atomParameters[atom].second;
        if (atomEpsilon != 0.0f) {
            fvec4 sig = blockAtomSigma+atomParameters[atom].first;
            fvec4 sig2 = inverseR*sig;
            sig2 *= sig2;
            fvec4 sig6 = sig2*sig2*sig2;
            fvec4 epsSig6 = blockAtomEpsilon*atomEpsilon*sig6;
            dEdR = epsSig6*(12.0f*sig6 - 6.0f);
            energy = epsSig6*(sig6-1.0f);
            if (useSwitch) {
                fvec4 t = (r>switchingDistance) & ((r-switchingDistance)*invSwitchingInterval);
                fvec4 switchValue = 1+t*t*t*(-10.0f+t*(15.0f-t*6.0f));
                fvec4 switchDeriv = t*t*(-30.0f+t*(60.0f-t*30.0f))*invSwitchingInterval;
                dEdR = switchValue*dEdR - energy*switchDeriv*r;
                energy *= switchValue;
            }
        }
        else {
            energy = 0.0f;
            dEdR = 0.0f;
        }
        fvec4 chargeProd = blockAtomCharge*posq[4*atom+3];
        dEdR += chargeProd*inverseR*ewaldScaleFunction(r);
        dEdR *= inverseR*inverseR;        

        // Accumulate energies.

        fvec4 one(1.0f);
        if (totalEnergy) {
            energy += chargeProd*inverseR*erfcApprox(alphaEwald*r);
            energy = blend(0.0f, energy, include);
            *totalEnergy += dot4(energy, one);
        }

        // Accumulate forces.

        dEdR = blend(0.0f, dEdR, include);
        fvec4 fx = dx*dEdR;
        fvec4 fy = dy*dEdR;
        fvec4 fz = dz*dEdR;
        blockAtomForceX += fx;
        blockAtomForceY += fy;
        blockAtomForceZ += fz;
        float* atomForce = forces+4*atom;
        atomForce[0] -= dot4(fx, one);
        atomForce[1] -= dot4(fy, one);
        atomForce[2] -= dot4(fz, one);
    }
    
    // Record the forces on the block atoms.
    
    fvec4 f[4] = {blockAtomForceX, blockAtomForceY, blockAtomForceZ, 0.0f};
    transpose(f[0], f[1], f[2], f[3]);
    for (int j = 0; j < 4; j++)
        (fvec4(forces+4*blockAtom[j])+f[j]).store(forces+4*blockAtom[j]);
}

void CpuNonbondedForceVec4::getDeltaR(const float* posI, const fvec4& x, const fvec4& y, const fvec4& z, fvec4& dx, fvec4& dy, fvec4& dz, fvec4& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const {
    dx = x-posI[0];
    dy = y-posI[1];
    dz = z-posI[2];
    if (periodic) {
        dx -= round(dx*invBoxSize[0])*boxSize[0];
        dy -= round(dy*invBoxSize[1])*boxSize[1];
        dz -= round(dz*invBoxSize[2])*boxSize[2];
    }
    r2 = dx*dx + dy*dy + dz*dz;
}

fvec4 CpuNonbondedForceVec4::erfcApprox(fvec4 x) {
    // This approximation for erfc is from Abramowitz and Stegun (1964) p. 299.  They cite the following as
    // the original source: C. Hastings, Jr., Approximations for Digital Computers (1955).  It has a maximum
    // error of 3e-7.

    fvec4 t = 1.0f+(0.0705230784f+(0.0422820123f+(0.0092705272f+(0.0001520143f+(0.0002765672f+0.0000430638f*x)*x)*x)*x)*x)*x;
    t *= t;
    t *= t;
    t *= t;
    return 1.0f/(t*t);
}

fvec4 CpuNonbondedForceVec4::ewaldScaleFunction(fvec4 x) {
    // Compute the tabulated Ewald scale factor: erfc(alpha*r) + 2*alpha*r*exp(-alpha*alpha*r*r)/sqrt(PI)

    fvec4 x1 = x*ewaldDXInv;
    ivec4 index = min(floor(x1), NUM_TABLE_POINTS);
    fvec4 coeff2 = x1-index;
    fvec4 coeff1 = 1.0f-coeff2;
    fvec4 t1(&ewaldScaleTable[index[0]]);
    fvec4 t2(&ewaldScaleTable[index[1]]);
    fvec4 t3(&ewaldScaleTable[index[2]]);
    fvec4 t4(&ewaldScaleTable[index[3]]);
    transpose(t1, t2, t3, t4);
    return coeff1*t1 + coeff2*t2;
}