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-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "nbnxn_kernel_gpu_ref.h"
+
+#include "config.h"
#include <math.h>
-#include "types/simple.h"
-#include "maths.h"
-#include "vec.h"
-#include "typedefs.h"
-#include "force.h"
-#include "nbnxn_kernel_gpu_ref.h"
-#include "../nbnxn_consts.h"
-#include "nbnxn_kernel_common.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
+#include "gromacs/pbcutil/ishift.h"
#define NCL_PER_SUPERCL (NBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER)
#define CL_SIZE (NBNXN_GPU_CLUSTER_SIZE)
const nbnxn_atomdata_t *nbat,
const interaction_const_t *iconst,
rvec *shift_vec,
- int force_flags,
- int clearF,
- real * f,
- real * fshift,
- real * Vc,
- real * Vvdw)
+ int force_flags,
+ int clearF,
+ real * f,
+ real * fshift,
+ real * Vc,
+ real * Vvdw)
{
- const nbnxn_sci_t *nbln;
- const real *x;
- gmx_bool bEner;
- gmx_bool bEwald;
- const real *Ftab=NULL;
- real rcut2,rvdw2,rlist2;
- int ntype;
- real facel;
- int n;
- int ish3;
- int sci;
- int cj4_ind0,cj4_ind1,cj4_ind;
- int ci,cj;
- int ic,jc,ia,ja,is,ifs,js,jfs,im,jm;
- int n0;
- int ggid;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real iq;
- real qq,vcoul=0,krsq,vctot;
- int nti;
- int tj;
- real rt,r,eps;
- real rinvsix;
- real Vvdwtot;
- real Vvdw_rep,Vvdw_disp;
- real ix,iy,iz,fix,fiy,fiz;
- real jx,jy,jz;
- real dx,dy,dz,rsq,rinv;
- int int_bit;
- real fexcl;
- real c6,c12,cexp1,cexp2,br;
- const real * shiftvec;
- real * vdwparam;
- int * shift;
- int * type;
+ const nbnxn_sci_t *nbln;
+ const real *x;
+ gmx_bool bEner;
+ gmx_bool bEwald;
+ const real *Ftab = NULL;
+ real rcut2, rvdw2, rlist2;
+ int ntype;
+ real facel;
+ int n;
+ int ish3;
+ int sci;
+ int cj4_ind0, cj4_ind1, cj4_ind;
+ int ci, cj;
+ int ic, jc, ia, ja, is, ifs, js, jfs, im, jm;
+ int n0;
+ int ggid;
+ real shX, shY, shZ;
+ real fscal, tx, ty, tz;
+ real rinvsq;
+ real iq;
+ real qq, vcoul = 0, krsq, vctot;
+ int nti;
+ int tj;
+ real rt, r, eps;
+ real rinvsix;
+ real Vvdwtot;
+ real Vvdw_rep, Vvdw_disp;
+ real ix, iy, iz, fix, fiy, fiz;
+ real jx, jy, jz;
+ real dx, dy, dz, rsq, rinv;
+ int int_bit;
+ real fexcl;
+ real c6, c12, cexp1, cexp2, br;
+ const real * shiftvec;
+ real * vdwparam;
+ int * shift;
+ int * type;
const nbnxn_excl_t *excl[2];
- int npair_tot,npair;
- int nhwu,nhwu_pruned;
+ int npair_tot, npair;
+ int nhwu, nhwu_pruned;
if (nbl->na_ci != CL_SIZE)
{
- gmx_fatal(FARGS,"The neighborlist cluster size in the GPU reference kernel is %d, expected it to be %d",nbl->na_ci,CL_SIZE);
+ gmx_fatal(FARGS, "The neighborlist cluster size in the GPU reference kernel is %d, expected it to be %d", nbl->na_ci, CL_SIZE);
}
if (clearF == enbvClearFYes)
{
- clear_f(nbat, f);
+ clear_f(nbat, 0, f);
}
bEner = (force_flags & GMX_FORCE_ENERGY);
nhwu = 0;
nhwu_pruned = 0;
- for(n=0; n<nbl->nsci; n++)
+ for (n = 0; n < nbl->nsci; n++)
{
nbln = &nbl->sci[n];
- ish3 = 3*nbln->shift;
- shX = shiftvec[ish3];
+ ish3 = 3*nbln->shift;
+ shX = shiftvec[ish3];
shY = shiftvec[ish3+1];
shZ = shiftvec[ish3+2];
- cj4_ind0 = nbln->cj4_ind_start;
- cj4_ind1 = nbln->cj4_ind_end;
+ cj4_ind0 = nbln->cj4_ind_start;
+ cj4_ind1 = nbln->cj4_ind_end;
sci = nbln->sci;
- vctot = 0;
- Vvdwtot = 0;
+ vctot = 0;
+ Vvdwtot = 0;
if (nbln->shift == CENTRAL &&
nbl->cj4[cj4_ind0].cj[0] == sci*NCL_PER_SUPERCL)
/* we have the diagonal:
* add the charge self interaction energy term
*/
- for(im=0; im<NCL_PER_SUPERCL; im++)
+ for (im = 0; im < NCL_PER_SUPERCL; im++)
{
ci = sci*NCL_PER_SUPERCL + im;
- for (ic=0; ic<CL_SIZE; ic++)
+ for (ic = 0; ic < CL_SIZE; ic++)
{
ia = ci*CL_SIZE + ic;
iq = x[ia*nbat->xstride+3];
else
{
/* last factor 1/sqrt(pi) */
- vctot *= -facel*iconst->ewaldcoeff*0.564189583548;
+ vctot *= -facel*iconst->ewaldcoeff_q*M_1_SQRTPI;
}
}
-
- for(cj4_ind=cj4_ind0; (cj4_ind<cj4_ind1); cj4_ind++)
+
+ for (cj4_ind = cj4_ind0; (cj4_ind < cj4_ind1); cj4_ind++)
{
excl[0] = &nbl->excl[nbl->cj4[cj4_ind].imei[0].excl_ind];
excl[1] = &nbl->excl[nbl->cj4[cj4_ind].imei[1].excl_ind];
- for(jm=0; jm<4; jm++)
+ for (jm = 0; jm < NBNXN_GPU_JGROUP_SIZE; jm++)
{
cj = nbl->cj4[cj4_ind].cj[jm];
- for(im=0; im<NCL_PER_SUPERCL; im++)
+ for (im = 0; im < NCL_PER_SUPERCL; im++)
{
/* We're only using the first imask,
* but here imei[1].imask is identical.
within_rlist = FALSE;
npair = 0;
- for(ic=0; ic<CL_SIZE; ic++)
+ for (ic = 0; ic < CL_SIZE; ic++)
{
ia = ci*CL_SIZE + ic;
-
+
is = ia*nbat->xstride;
ifs = ia*nbat->fstride;
ix = shX + x[is+0];
iz = shZ + x[is+2];
iq = facel*x[is+3];
nti = ntype*2*type[ia];
-
+
fix = 0;
fiy = 0;
fiz = 0;
- for(jc=0; jc<CL_SIZE; jc++)
+ for (jc = 0; jc < CL_SIZE; jc++)
{
ja = cj*CL_SIZE + jc;
{
continue;
}
-
- int_bit = ((excl[jc>>2]->pair[(jc & 3)*CL_SIZE+ic] >> (jm*NCL_PER_SUPERCL+im)) & 1);
+
+ int_bit = ((excl[jc>>2]->pair[(jc & 3)*CL_SIZE+ic] >> (jm*NCL_PER_SUPERCL+im)) & 1);
js = ja*nbat->xstride;
jfs = ja*nbat->fstride;
- jx = x[js+0];
- jy = x[js+1];
- jz = x[js+2];
- dx = ix - jx;
- dy = iy - jy;
- dz = iz - jz;
+ jx = x[js+0];
+ jy = x[js+1];
+ jz = x[js+2];
+ dx = ix - jx;
+ dy = iy - jy;
+ dz = iz - jz;
rsq = dx*dx + dy*dy + dz*dz;
if (rsq < rlist2)
{
rsq += (1.0 - int_bit)*NBNXN_AVOID_SING_R2_INC;
rinv = gmx_invsqrt(rsq);
- rinvsq = rinv*rinv;
+ rinvsq = rinv*rinv;
fscal = 0;
-
+
qq = iq*x[js+3];
if (!bEwald)
{
if (bEner)
{
- vcoul = qq*((int_bit - gmx_erf(iconst->ewaldcoeff*r))*rinv - int_bit*iconst->sh_ewald);
+ vcoul = qq*((int_bit - gmx_erf(iconst->ewaldcoeff_q*r))*rinv - int_bit*iconst->sh_ewald);
}
}
/* Vanilla Lennard-Jones cutoff */
c6 = vdwparam[tj];
c12 = vdwparam[tj+1];
-
+
rinvsix = int_bit*rinvsq*rinvsq*rinvsq;
- Vvdw_disp = c6*rinvsix;
+ Vvdw_disp = c6*rinvsix;
Vvdw_rep = c12*rinvsix*rinvsix;
fscal += (Vvdw_rep - Vvdw_disp)*rinvsq;
(Vvdw_disp - int_bit*c6*iconst->sh_invrc6)/6;
}
}
-
+
tx = fscal*dx;
ty = fscal*dy;
tz = fscal*dz;
f[jfs+1] -= ty;
f[jfs+2] -= tz;
}
-
+
f[ifs+0] += fix;
f[ifs+1] += fiy;
f[ifs+2] += fiz;
}
}
}
-
+
if (bEner)
{
- ggid = 0;
+ ggid = 0;
Vc[ggid] = Vc[ggid] + vctot;
Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
}
if (debug)
{
- fprintf(debug,"number of half %dx%d atom pairs: %d after pruning: %d fraction %4.2f\n",
- nbl->na_ci,nbl->na_ci,
- nhwu,nhwu_pruned,nhwu_pruned/(double)nhwu);
- fprintf(debug,"generic kernel pair interactions: %d\n",
+ fprintf(debug, "number of half %dx%d atom pairs: %d after pruning: %d fraction %4.2f\n",
+ nbl->na_ci, nbl->na_ci,
+ nhwu, nhwu_pruned, nhwu_pruned/(double)nhwu);
+ fprintf(debug, "generic kernel pair interactions: %d\n",
nhwu*nbl->na_ci/2*nbl->na_ci);
- fprintf(debug,"generic kernel post-prune pair interactions: %d\n",
+ fprintf(debug, "generic kernel post-prune pair interactions: %d\n",
nhwu_pruned*nbl->na_ci/2*nbl->na_ci);
- fprintf(debug,"generic kernel non-zero pair interactions: %d\n",
+ fprintf(debug, "generic kernel non-zero pair interactions: %d\n",
npair_tot);
- fprintf(debug,"ratio non-zero/post-prune pair interactions: %4.2f\n",
+ fprintf(debug, "ratio non-zero/post-prune pair interactions: %4.2f\n",
npair_tot/(double)(nhwu_pruned*nbl->na_ci/2*nbl->na_ci));
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff