void
nb_kernel_allvsall(t_forcerec * fr,
t_mdatoms * mdatoms,
t_blocka * excl,
real * x,
real * f,
real * Vc,
real * Vvdw,
int * outeriter,
int * inneriter,
void * work)
{
gmx_allvsall_data_t *aadata;
int natoms;
int ni0,ni1;
int nj0,nj1,nj2;
int i,j,k;
real * charge;
int * type;
real facel;
real * pvdw;
int ggid;
int * mask;
real ix,iy,iz,iq;
real fix,fiy,fiz;
real jx,jy,jz,qq;
real dx,dy,dz;
real tx,ty,tz;
real rsq,rinv,rinvsq,rinvsix;
real vcoul,vctot;
real c6,c12,Vvdw6,Vvdw12,Vvdwtot;
real fscal;
charge = mdatoms->chargeA;
type = mdatoms->typeA;
facel = fr->epsfac;
natoms = mdatoms->nr;
ni0 = mdatoms->start;
ni1 = mdatoms->start+mdatoms->homenr;
aadata = *((gmx_allvsall_data_t **)work);
if(aadata==NULL)
{
setup_aadata(&aadata,excl,natoms,type,fr->ntype,fr->nbfp);
*((gmx_allvsall_data_t **)work) = aadata;
}
for(i=ni0; i<ni1; i++)
{
/* We assume shifts are NOT used for all-vs-all interactions */
/* Load i atom data */
ix = x[3*i];
iy = x[3*i+1];
iz = x[3*i+2];
iq = facel*charge[i];
pvdw = aadata->pvdwparam[type[i]];
/* Zero the potential energy for this list */
Vvdwtot = 0.0;
vctot = 0.0;
/* Clear i atom forces */
fix = 0.0;
fiy = 0.0;
fiz = 0.0;
/* Load limits for loop over neighbors */
nj0 = aadata->jindex[3*i];
nj1 = aadata->jindex[3*i+1];
nj2 = aadata->jindex[3*i+2];
mask = aadata->exclusion_mask[i];
/* Prologue part, including exclusion mask */
for(j=nj0; j<nj1; j++,mask++)
{
if(*mask!=0)
{
k = j%natoms;
/* load j atom coordinates */
jx = x[3*k];
jy = x[3*k+1];
jz = x[3*k+2];
/* Calculate distance */
dx = ix - jx;
dy = iy - jy;
dz = iz - jz;
rsq = dx*dx+dy*dy+dz*dz;
/* Calculate 1/r and 1/r2 */
rinv = gmx_invsqrt(rsq);
rinvsq = rinv*rinv;
/* Load parameters for j atom */
qq = iq*charge[k];
c6 = pvdw[2*k];
c12 = pvdw[2*k+1];
/* Coulomb interaction */
vcoul = qq*rinv;
vctot = vctot+vcoul;
/* Lennard-Jones interaction */
rinvsix = rinvsq*rinvsq*rinvsq;
Vvdw6 = c6*rinvsix;
Vvdw12 = c12*rinvsix*rinvsix;
Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
fscal = (vcoul+12.0*Vvdw12-6.0*Vvdw6)*rinvsq;
/* Calculate temporary vectorial force */
tx = fscal*dx;
ty = fscal*dy;
tz = fscal*dz;
/* Increment i atom force */
fix = fix + tx;
fiy = fiy + ty;
fiz = fiz + tz;
/* Decrement j atom force */
f[3*k] = f[3*k] - tx;
f[3*k+1] = f[3*k+1] - ty;
f[3*k+2] = f[3*k+2] - tz;
}
/* Inner loop uses 38 flops/iteration */
}
/* Main part, no exclusions */
for(j=nj1; j<nj2; j++)
{
k = j%natoms;
/* load j atom coordinates */
jx = x[3*k];
jy = x[3*k+1];
jz = x[3*k+2];
/* Calculate distance */
dx = ix - jx;
dy = iy - jy;
dz = iz - jz;
rsq = dx*dx+dy*dy+dz*dz;
/* Calculate 1/r and 1/r2 */
rinv = gmx_invsqrt(rsq);
rinvsq = rinv*rinv;
/* Load parameters for j atom */
qq = iq*charge[k];
c6 = pvdw[2*k];
c12 = pvdw[2*k+1];
/* Coulomb interaction */
vcoul = qq*rinv;
vctot = vctot+vcoul;
/* Lennard-Jones interaction */
rinvsix = rinvsq*rinvsq*rinvsq;
Vvdw6 = c6*rinvsix;
Vvdw12 = c12*rinvsix*rinvsix;
Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
fscal = (vcoul+12.0*Vvdw12-6.0*Vvdw6)*rinvsq;
/* Calculate temporary vectorial force */
tx = fscal*dx;
ty = fscal*dy;
tz = fscal*dz;
/* Increment i atom force */
fix = fix + tx;
fiy = fiy + ty;
fiz = fiz + tz;
/* Decrement j atom force */
f[3*k] = f[3*k] - tx;
f[3*k+1] = f[3*k+1] - ty;
f[3*k+2] = f[3*k+2] - tz;
/* Inner loop uses 38 flops/iteration */
}
f[3*i] += fix;
f[3*i+1] += fiy;
f[3*i+2] += fiz;
/* Add potential energies to the group for this list */
ggid = 0;
Vc[ggid] = Vc[ggid] + vctot;
Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
/* Outer loop uses 6 flops/iteration */
}
/* Write outer/inner iteration count to pointers */
*outeriter = ni1-ni0;
*inneriter = (ni1-ni0)*natoms/2;
}
void
nb_kernel_allvsallgb(t_forcerec * fr,
t_mdatoms * mdatoms,
t_blocka * excl,
real * x,
real * f,
real * Vc,
real * Vvdw,
real * vpol,
int * outeriter,
int * inneriter,
void * work)
{
gmx_allvsall_data_t *aadata;
int natoms;
int ni0,ni1;
int nj0,nj1,nj2;
int i,j,k;
real * charge;
int * type;
real facel;
real * pvdw;
int ggid;
int * mask;
real * GBtab;
real gbfactor;
real * invsqrta;
real * dvda;
real vgbtot,dvdasum;
int nnn,n0;
real ix,iy,iz,iq;
real fix,fiy,fiz;
real jx,jy,jz,qq;
real dx,dy,dz;
real tx,ty,tz;
real rsq,rinv,rinvsq,rinvsix;
real vcoul,vctot;
real c6,c12,Vvdw6,Vvdw12,Vvdwtot;
real fscal,dvdatmp,fijC,vgb;
real Y,F,Fp,Geps,Heps2,VV,FF,eps,eps2,r,rt;
real dvdaj,gbscale,isaprod,isai,isaj,gbtabscale;
charge = mdatoms->chargeA;
type = mdatoms->typeA;
gbfactor = ((1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
facel = fr->epsfac;
GBtab = fr->gbtab.tab;
gbtabscale = fr->gbtab.scale;
invsqrta = fr->invsqrta;
dvda = fr->dvda;
natoms = mdatoms->nr;
ni0 = mdatoms->start;
ni1 = mdatoms->start+mdatoms->homenr;
aadata = *((gmx_allvsall_data_t **)work);
if(aadata==NULL)
{
setup_aadata(&aadata,excl,natoms,type,fr->ntype,fr->nbfp);
*((gmx_allvsall_data_t **)work) = aadata;
}
for(i=ni0; i<ni1; i++)
{
/* We assume shifts are NOT used for all-vs-all interactions */
/* Load i atom data */
ix = x[3*i];
iy = x[3*i+1];
iz = x[3*i+2];
iq = facel*charge[i];
isai = invsqrta[i];
pvdw = aadata->pvdwparam[type[i]];
/* Zero the potential energy for this list */
Vvdwtot = 0.0;
vctot = 0.0;
vgbtot = 0.0;
dvdasum = 0.0;
/* Clear i atom forces */
fix = 0.0;
fiy = 0.0;
fiz = 0.0;
/* Load limits for loop over neighbors */
nj0 = aadata->jindex[3*i];
nj1 = aadata->jindex[3*i+1];
nj2 = aadata->jindex[3*i+2];
mask = aadata->exclusion_mask[i];
/* Prologue part, including exclusion mask */
for(j=nj0; j<nj1; j++,mask++)
{
if(*mask!=0)
{
k = j%natoms;
/* load j atom coordinates */
jx = x[3*k];
jy = x[3*k+1];
jz = x[3*k+2];
/* Calculate distance */
dx = ix - jx;
dy = iy - jy;
dz = iz - jz;
rsq = dx*dx+dy*dy+dz*dz;
/* Calculate 1/r and 1/r2 */
rinv = gmx_invsqrt(rsq);
/* Load parameters for j atom */
isaj = invsqrta[k];
isaprod = isai*isaj;
qq = iq*charge[k];
vcoul = qq*rinv;
fscal = vcoul*rinv;
qq = isaprod*(-qq)*gbfactor;
gbscale = isaprod*gbtabscale;
c6 = pvdw[2*k];
c12 = pvdw[2*k+1];
rinvsq = rinv*rinv;
/* Tabulated Generalized-Born interaction */
dvdaj = dvda[k];
r = rsq*rinv;
/* Calculate table index */
rt = r*gbscale;
n0 = rt;
eps = rt-n0;
eps2 = eps*eps;
nnn = 4*n0;
Y = GBtab[nnn];
F = GBtab[nnn+1];
Geps = eps*GBtab[nnn+2];
Heps2 = eps2*GBtab[nnn+3];
Fp = F+Geps+Heps2;
VV = Y+eps*Fp;
FF = Fp+Geps+2.0*Heps2;
vgb = qq*VV;
fijC = qq*FF*gbscale;
dvdatmp = -0.5*(vgb+fijC*r);
dvdasum = dvdasum + dvdatmp;
dvda[k] = dvdaj+dvdatmp*isaj*isaj;
vctot = vctot + vcoul;
vgbtot = vgbtot + vgb;
/* Lennard-Jones interaction */
rinvsix = rinvsq*rinvsq*rinvsq;
Vvdw6 = c6*rinvsix;
Vvdw12 = c12*rinvsix*rinvsix;
Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
fscal = (12.0*Vvdw12-6.0*Vvdw6)*rinvsq-(fijC-fscal)*rinv;
/* Calculate temporary vectorial force */
tx = fscal*dx;
ty = fscal*dy;
tz = fscal*dz;
/* Increment i atom force */
fix = fix + tx;
fiy = fiy + ty;
fiz = fiz + tz;
/* Decrement j atom force */
f[3*k] = f[3*k] - tx;
f[3*k+1] = f[3*k+1] - ty;
f[3*k+2] = f[3*k+2] - tz;
}
/* Inner loop uses 38 flops/iteration */
}
/* Main part, no exclusions */
for(j=nj1; j<nj2; j++)
{
k = j%natoms;
/* load j atom coordinates */
jx = x[3*k];
jy = x[3*k+1];
jz = x[3*k+2];
/* Calculate distance */
dx = ix - jx;
dy = iy - jy;
dz = iz - jz;
rsq = dx*dx+dy*dy+dz*dz;
/* Calculate 1/r and 1/r2 */
rinv = gmx_invsqrt(rsq);
/* Load parameters for j atom */
isaj = invsqrta[k];
isaprod = isai*isaj;
qq = iq*charge[k];
vcoul = qq*rinv;
fscal = vcoul*rinv;
qq = isaprod*(-qq)*gbfactor;
gbscale = isaprod*gbtabscale;
c6 = pvdw[2*k];
c12 = pvdw[2*k+1];
rinvsq = rinv*rinv;
/* Tabulated Generalized-Born interaction */
dvdaj = dvda[k];
r = rsq*rinv;
/* Calculate table index */
rt = r*gbscale;
n0 = rt;
eps = rt-n0;
eps2 = eps*eps;
nnn = 4*n0;
Y = GBtab[nnn];
F = GBtab[nnn+1];
Geps = eps*GBtab[nnn+2];
Heps2 = eps2*GBtab[nnn+3];
Fp = F+Geps+Heps2;
VV = Y+eps*Fp;
FF = Fp+Geps+2.0*Heps2;
vgb = qq*VV;
fijC = qq*FF*gbscale;
dvdatmp = -0.5*(vgb+fijC*r);
dvdasum = dvdasum + dvdatmp;
dvda[k] = dvdaj+dvdatmp*isaj*isaj;
vctot = vctot + vcoul;
vgbtot = vgbtot + vgb;
/* Lennard-Jones interaction */
rinvsix = rinvsq*rinvsq*rinvsq;
Vvdw6 = c6*rinvsix;
Vvdw12 = c12*rinvsix*rinvsix;
Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
fscal = (12.0*Vvdw12-6.0*Vvdw6)*rinvsq-(fijC-fscal)*rinv;
/* Calculate temporary vectorial force */
tx = fscal*dx;
ty = fscal*dy;
tz = fscal*dz;
/* Increment i atom force */
fix = fix + tx;
fiy = fiy + ty;
fiz = fiz + tz;
/* Decrement j atom force */
f[3*k] = f[3*k] - tx;
f[3*k+1] = f[3*k+1] - ty;
f[3*k+2] = f[3*k+2] - tz;
/* Inner loop uses 38 flops/iteration */
}
f[3*i] += fix;
f[3*i+1] += fiy;
f[3*i+2] += fiz;
/* Add potential energies to the group for this list */
ggid = 0;
Vc[ggid] = Vc[ggid] + vctot;
Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
vpol[ggid] = vpol[ggid] + vgbtot;
dvda[i] = dvda[i] + dvdasum*isai*isai;
/* Outer loop uses 6 flops/iteration */
}
/* Write outer/inner iteration count to pointers */
*outeriter = ni1-ni0;
*inneriter = (ni1-ni0)*natoms/2;
}
void
nb_kernel_allvsall(t_nblist gmx_unused * nlist,
rvec * xx,
rvec * ff,
struct t_forcerec * fr,
t_mdatoms * mdatoms,
nb_kernel_data_t * kernel_data,
t_nrnb * nrnb)
{
gmx_allvsall_data_t *aadata;
int natoms;
int ni0, ni1;
int nj0, nj1, nj2;
int i, j, k;
real * charge;
int * type;
real facel;
real * pvdw;
int ggid;
int * mask;
real ix, iy, iz, iq;
real fix, fiy, fiz;
real jx, jy, jz, qq;
real dx, dy, dz;
real tx, ty, tz;
real rsq, rinv, rinvsq, rinvsix;
real vcoul, vctot;
real c6, c12, Vvdw6, Vvdw12, Vvdwtot;
real fscal;
const t_blocka *excl;
real * f;
real * x;
real * Vvdw;
real * Vc;
x = xx[0];
f = ff[0];
charge = mdatoms->chargeA;
type = mdatoms->typeA;
facel = fr->ic->epsfac;
natoms = mdatoms->nr;
ni0 = 0;
ni1 = mdatoms->homenr;
aadata = reinterpret_cast<gmx_allvsall_data_t *>(fr->AllvsAll_work);
excl = kernel_data->exclusions;
Vc = kernel_data->energygrp_elec;
Vvdw = kernel_data->energygrp_vdw;
if (aadata == nullptr)
{
setup_aadata(&aadata, excl, natoms, type, fr->ntype, fr->nbfp);
fr->AllvsAll_work = aadata;
}
for (i = ni0; i < ni1; i++)
{
/* We assume shifts are NOT used for all-vs-all interactions */
/* Load i atom data */
ix = x[3*i];
iy = x[3*i+1];
iz = x[3*i+2];
iq = facel*charge[i];
pvdw = aadata->pvdwparam[type[i]];
/* Zero the potential energy for this list */
Vvdwtot = 0.0;
vctot = 0.0;
/* Clear i atom forces */
fix = 0.0;
fiy = 0.0;
fiz = 0.0;
/* Load limits for loop over neighbors */
nj0 = aadata->jindex[3*i];
nj1 = aadata->jindex[3*i+1];
nj2 = aadata->jindex[3*i+2];
mask = aadata->exclusion_mask[i];
/* Prologue part, including exclusion mask */
for (j = nj0; j < nj1; j++, mask++)
{
if (*mask != 0)
{
k = j%natoms;
/* load j atom coordinates */
jx = x[3*k];
jy = x[3*k+1];
jz = x[3*k+2];
/* Calculate distance */
dx = ix - jx;
dy = iy - jy;
dz = iz - jz;
rsq = dx*dx+dy*dy+dz*dz;
/* Calculate 1/r and 1/r2 */
rinv = 1.0/sqrt(rsq);
rinvsq = rinv*rinv;
/* Load parameters for j atom */
qq = iq*charge[k];
c6 = pvdw[2*k];
c12 = pvdw[2*k+1];
/* Coulomb interaction */
vcoul = qq*rinv;
vctot = vctot+vcoul;
/* Lennard-Jones interaction */
rinvsix = rinvsq*rinvsq*rinvsq;
Vvdw6 = c6*rinvsix;
Vvdw12 = c12*rinvsix*rinvsix;
Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
fscal = (vcoul+12.0*Vvdw12-6.0*Vvdw6)*rinvsq;
/* Calculate temporary vectorial force */
tx = fscal*dx;
ty = fscal*dy;
tz = fscal*dz;
/* Increment i atom force */
fix = fix + tx;
fiy = fiy + ty;
fiz = fiz + tz;
/* Decrement j atom force */
f[3*k] = f[3*k] - tx;
f[3*k+1] = f[3*k+1] - ty;
f[3*k+2] = f[3*k+2] - tz;
}
/* Inner loop uses 38 flops/iteration */
}
/* Main part, no exclusions */
for (j = nj1; j < nj2; j++)
{
k = j%natoms;
/* load j atom coordinates */
jx = x[3*k];
jy = x[3*k+1];
jz = x[3*k+2];
/* Calculate distance */
dx = ix - jx;
dy = iy - jy;
dz = iz - jz;
rsq = dx*dx+dy*dy+dz*dz;
/* Calculate 1/r and 1/r2 */
rinv = 1.0/sqrt(rsq);
rinvsq = rinv*rinv;
/* Load parameters for j atom */
qq = iq*charge[k];
c6 = pvdw[2*k];
c12 = pvdw[2*k+1];
/* Coulomb interaction */
vcoul = qq*rinv;
vctot = vctot+vcoul;
/* Lennard-Jones interaction */
rinvsix = rinvsq*rinvsq*rinvsq;
Vvdw6 = c6*rinvsix;
Vvdw12 = c12*rinvsix*rinvsix;
Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
fscal = (vcoul+12.0*Vvdw12-6.0*Vvdw6)*rinvsq;
/* Calculate temporary vectorial force */
tx = fscal*dx;
ty = fscal*dy;
tz = fscal*dz;
/* Increment i atom force */
fix = fix + tx;
fiy = fiy + ty;
fiz = fiz + tz;
/* Decrement j atom force */
f[3*k] = f[3*k] - tx;
f[3*k+1] = f[3*k+1] - ty;
f[3*k+2] = f[3*k+2] - tz;
/* Inner loop uses 38 flops/iteration */
}
f[3*i] += fix;
f[3*i+1] += fiy;
f[3*i+2] += fiz;
/* Add potential energies to the group for this list */
ggid = 0;
Vc[ggid] = Vc[ggid] + vctot;
Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
/* Outer loop uses 6 flops/iteration */
}
/* 12 flops per outer iteration
* 19 flops per inner iteration
*/
inc_nrnb(nrnb, eNR_NBKERNEL_ELEC_VDW_VF, (ni1-ni0)*12 + gmx::exactDiv(natoms*(natoms-1), 2)*19);
}
