#include "gmx_omp_nthreads.h"
/* Default nbnxn allocation routine, allocates NBNXN_MEM_ALIGN byte aligned */
-void nbnxn_alloc_aligned(void **ptr,size_t nbytes)
+void nbnxn_alloc_aligned(void **ptr, size_t nbytes)
{
- *ptr = save_malloc_aligned("ptr",__FILE__,__LINE__,nbytes,1,NBNXN_MEM_ALIGN);
+ *ptr = save_malloc_aligned("ptr", __FILE__, __LINE__, nbytes, 1, NBNXN_MEM_ALIGN);
}
/* Free function for memory allocated with nbnxn_alloc_aligned */
/* Reallocation wrapper function for nbnxn data structures */
void nbnxn_realloc_void(void **ptr,
- int nbytes_copy,int nbytes_new,
+ int nbytes_copy, int nbytes_new,
nbnxn_alloc_t *ma,
nbnxn_free_t *mf)
{
void *ptr_new;
- ma(&ptr_new,nbytes_new);
+ ma(&ptr_new, nbytes_new);
if (nbytes_new > 0 && ptr_new == NULL)
{
{
gmx_incons("In nbnxn_realloc_void: new size less than copy size");
}
- memcpy(ptr_new,*ptr,nbytes_copy);
+ memcpy(ptr_new, *ptr, nbytes_copy);
}
if (*ptr != NULL)
{
}
/* Reallocate the nbnxn_atomdata_t for a size of n atoms */
-void nbnxn_atomdata_realloc(nbnxn_atomdata_t *nbat,int n)
+void nbnxn_atomdata_realloc(nbnxn_atomdata_t *nbat, int n)
{
int t;
nbnxn_realloc_void((void **)&nbat->type,
nbat->natoms*sizeof(*nbat->type),
n*sizeof(*nbat->type),
- nbat->alloc,nbat->free);
+ nbat->alloc, nbat->free);
nbnxn_realloc_void((void **)&nbat->lj_comb,
nbat->natoms*2*sizeof(*nbat->lj_comb),
n*2*sizeof(*nbat->lj_comb),
- nbat->alloc,nbat->free);
+ nbat->alloc, nbat->free);
if (nbat->XFormat != nbatXYZQ)
{
nbnxn_realloc_void((void **)&nbat->q,
nbat->natoms*sizeof(*nbat->q),
n*sizeof(*nbat->q),
- nbat->alloc,nbat->free);
+ nbat->alloc, nbat->free);
}
if (nbat->nenergrp > 1)
{
nbnxn_realloc_void((void **)&nbat->energrp,
nbat->natoms/nbat->na_c*sizeof(*nbat->energrp),
n/nbat->na_c*sizeof(*nbat->energrp),
- nbat->alloc,nbat->free);
+ nbat->alloc, nbat->free);
}
nbnxn_realloc_void((void **)&nbat->x,
nbat->natoms*nbat->xstride*sizeof(*nbat->x),
n*nbat->xstride*sizeof(*nbat->x),
- nbat->alloc,nbat->free);
- for(t=0; t<nbat->nout; t++)
+ nbat->alloc, nbat->free);
+ for (t = 0; t < nbat->nout; t++)
{
/* Allocate one element extra for possible signaling with CUDA */
nbnxn_realloc_void((void **)&nbat->out[t].f,
nbat->natoms*nbat->fstride*sizeof(*nbat->out[t].f),
n*nbat->fstride*sizeof(*nbat->out[t].f),
- nbat->alloc,nbat->free);
+ nbat->alloc, nbat->free);
}
nbat->nalloc = n;
}
/* Initializes an nbnxn_atomdata_output_t data structure */
static void nbnxn_atomdata_output_init(nbnxn_atomdata_output_t *out,
int nb_kernel_type,
- int nenergrp,int stride,
+ int nenergrp, int stride,
nbnxn_alloc_t *ma)
{
int cj_size;
out->f = NULL;
- ma((void **)&out->fshift,SHIFTS*DIM*sizeof(*out->fshift));
+ ma((void **)&out->fshift, SHIFTS*DIM*sizeof(*out->fshift));
out->nV = nenergrp*nenergrp;
- ma((void **)&out->Vvdw,out->nV*sizeof(*out->Vvdw));
- ma((void **)&out->Vc ,out->nV*sizeof(*out->Vc ));
+ ma((void **)&out->Vvdw, out->nV*sizeof(*out->Vvdw));
+ ma((void **)&out->Vc, out->nV*sizeof(*out->Vc ));
if (nb_kernel_type == nbnxnk4xN_SIMD_4xN ||
nb_kernel_type == nbnxnk4xN_SIMD_2xNN)
{
- cj_size = nbnxn_kernel_to_cj_size(nb_kernel_type);
+ cj_size = nbnxn_kernel_to_cj_size(nb_kernel_type);
out->nVS = nenergrp*nenergrp*stride*(cj_size>>1)*cj_size;
- ma((void **)&out->VSvdw,out->nVS*sizeof(*out->VSvdw));
- ma((void **)&out->VSc ,out->nVS*sizeof(*out->VSc ));
+ ma((void **)&out->VSvdw, out->nVS*sizeof(*out->VSvdw));
+ ma((void **)&out->VSc, out->nVS*sizeof(*out->VSc ));
}
else
{
}
}
-static void copy_int_to_nbat_int(const int *a,int na,int na_round,
- const int *in,int fill,int *innb)
+static void copy_int_to_nbat_int(const int *a, int na, int na_round,
+ const int *in, int fill, int *innb)
{
- int i,j;
+ int i, j;
j = 0;
- for(i=0; i<na; i++)
+ for (i = 0; i < na; i++)
{
innb[j++] = in[a[i]];
}
/* Complete the partially filled last cell with fill */
- for(; i<na_round; i++)
+ for (; i < na_round; i++)
{
innb[j++] = fill;
}
}
-static void clear_nbat_real(int na,int nbatFormat,real *xnb,int a0)
+static void clear_nbat_real(int na, int nbatFormat, real *xnb, int a0)
{
- int a,d,j,c;
+ int a, d, j, c;
switch (nbatFormat)
{
- case nbatXYZ:
- for(a=0; a<na; a++)
- {
- for(d=0; d<DIM; d++)
+ case nbatXYZ:
+ for (a = 0; a < na; a++)
{
- xnb[(a0+a)*STRIDE_XYZ+d] = 0;
+ for (d = 0; d < DIM; d++)
+ {
+ xnb[(a0+a)*STRIDE_XYZ+d] = 0;
+ }
}
- }
- break;
- case nbatXYZQ:
- for(a=0; a<na; a++)
- {
- for(d=0; d<DIM; d++)
+ break;
+ case nbatXYZQ:
+ for (a = 0; a < na; a++)
{
- xnb[(a0+a)*STRIDE_XYZQ+d] = 0;
+ for (d = 0; d < DIM; d++)
+ {
+ xnb[(a0+a)*STRIDE_XYZQ+d] = 0;
+ }
}
- }
- break;
- case nbatX4:
- j = X4_IND_A(a0);
- c = a0 & (PACK_X4-1);
- for(a=0; a<na; a++)
- {
- xnb[j+XX*PACK_X4] = 0;
- xnb[j+YY*PACK_X4] = 0;
- xnb[j+ZZ*PACK_X4] = 0;
- j++;
- c++;
- if (c == PACK_X4)
+ break;
+ case nbatX4:
+ j = X4_IND_A(a0);
+ c = a0 & (PACK_X4-1);
+ for (a = 0; a < na; a++)
{
- j += (DIM-1)*PACK_X4;
- c = 0;
+ xnb[j+XX*PACK_X4] = 0;
+ xnb[j+YY*PACK_X4] = 0;
+ xnb[j+ZZ*PACK_X4] = 0;
+ j++;
+ c++;
+ if (c == PACK_X4)
+ {
+ j += (DIM-1)*PACK_X4;
+ c = 0;
+ }
}
- }
- break;
- case nbatX8:
- j = X8_IND_A(a0);
- c = a0 & (PACK_X8-1);
- for(a=0; a<na; a++)
- {
- xnb[j+XX*PACK_X8] = 0;
- xnb[j+YY*PACK_X8] = 0;
- xnb[j+ZZ*PACK_X8] = 0;
- j++;
- c++;
- if (c == PACK_X8)
+ break;
+ case nbatX8:
+ j = X8_IND_A(a0);
+ c = a0 & (PACK_X8-1);
+ for (a = 0; a < na; a++)
{
- j += (DIM-1)*PACK_X8;
- c = 0;
+ xnb[j+XX*PACK_X8] = 0;
+ xnb[j+YY*PACK_X8] = 0;
+ xnb[j+ZZ*PACK_X8] = 0;
+ j++;
+ c++;
+ if (c == PACK_X8)
+ {
+ j += (DIM-1)*PACK_X8;
+ c = 0;
+ }
}
- }
- break;
+ break;
}
}
-void copy_rvec_to_nbat_real(const int *a,int na,int na_round,
- rvec *x,int nbatFormat,real *xnb,int a0,
- int cx,int cy,int cz)
+void copy_rvec_to_nbat_real(const int *a, int na, int na_round,
+ rvec *x, int nbatFormat, real *xnb, int a0,
+ int cx, int cy, int cz)
{
- int i,j,c;
+ int i, j, c;
/* We might need to place filler particles to fill up the cell to na_round.
* The coefficients (LJ and q) for such particles are zero.
switch (nbatFormat)
{
- case nbatXYZ:
- j = a0*STRIDE_XYZ;
- for(i=0; i<na; i++)
- {
- xnb[j++] = x[a[i]][XX];
- xnb[j++] = x[a[i]][YY];
- xnb[j++] = x[a[i]][ZZ];
- }
- /* Complete the partially filled last cell with copies of the last element.
- * This simplifies the bounding box calculation and avoid
- * numerical issues with atoms that are coincidentally close.
- */
- for(; i<na_round; i++)
- {
- xnb[j++] = -NBAT_FAR_AWAY*(1 + cx);
- xnb[j++] = -NBAT_FAR_AWAY*(1 + cy);
- xnb[j++] = -NBAT_FAR_AWAY*(1 + cz + i);
- }
- break;
- case nbatXYZQ:
- j = a0*STRIDE_XYZQ;
- for(i=0; i<na; i++)
- {
- xnb[j++] = x[a[i]][XX];
- xnb[j++] = x[a[i]][YY];
- xnb[j++] = x[a[i]][ZZ];
- j++;
- }
- /* Complete the partially filled last cell with particles far apart */
- for(; i<na_round; i++)
- {
- xnb[j++] = -NBAT_FAR_AWAY*(1 + cx);
- xnb[j++] = -NBAT_FAR_AWAY*(1 + cy);
- xnb[j++] = -NBAT_FAR_AWAY*(1 + cz + i);
- j++;
- }
- break;
- case nbatX4:
- j = X4_IND_A(a0);
- c = a0 & (PACK_X4-1);
- for(i=0; i<na; i++)
- {
- xnb[j+XX*PACK_X4] = x[a[i]][XX];
- xnb[j+YY*PACK_X4] = x[a[i]][YY];
- xnb[j+ZZ*PACK_X4] = x[a[i]][ZZ];
- j++;
- c++;
- if (c == PACK_X4)
+ case nbatXYZ:
+ j = a0*STRIDE_XYZ;
+ for (i = 0; i < na; i++)
{
- j += (DIM-1)*PACK_X4;
- c = 0;
+ xnb[j++] = x[a[i]][XX];
+ xnb[j++] = x[a[i]][YY];
+ xnb[j++] = x[a[i]][ZZ];
}
- }
- /* Complete the partially filled last cell with particles far apart */
- for(; i<na_round; i++)
- {
- xnb[j+XX*PACK_X4] = -NBAT_FAR_AWAY*(1 + cx);
- xnb[j+YY*PACK_X4] = -NBAT_FAR_AWAY*(1 + cy);
- xnb[j+ZZ*PACK_X4] = -NBAT_FAR_AWAY*(1 + cz + i);
- j++;
- c++;
- if (c == PACK_X4)
+ /* Complete the partially filled last cell with copies of the last element.
+ * This simplifies the bounding box calculation and avoid
+ * numerical issues with atoms that are coincidentally close.
+ */
+ for (; i < na_round; i++)
{
- j += (DIM-1)*PACK_X4;
- c = 0;
+ xnb[j++] = -NBAT_FAR_AWAY*(1 + cx);
+ xnb[j++] = -NBAT_FAR_AWAY*(1 + cy);
+ xnb[j++] = -NBAT_FAR_AWAY*(1 + cz + i);
}
- }
- break;
- case nbatX8:
- j = X8_IND_A(a0);
- c = a0 & (PACK_X8 - 1);
- for(i=0; i<na; i++)
- {
- xnb[j+XX*PACK_X8] = x[a[i]][XX];
- xnb[j+YY*PACK_X8] = x[a[i]][YY];
- xnb[j+ZZ*PACK_X8] = x[a[i]][ZZ];
- j++;
- c++;
- if (c == PACK_X8)
+ break;
+ case nbatXYZQ:
+ j = a0*STRIDE_XYZQ;
+ for (i = 0; i < na; i++)
{
- j += (DIM-1)*PACK_X8;
- c = 0;
+ xnb[j++] = x[a[i]][XX];
+ xnb[j++] = x[a[i]][YY];
+ xnb[j++] = x[a[i]][ZZ];
+ j++;
}
- }
- /* Complete the partially filled last cell with particles far apart */
- for(; i<na_round; i++)
- {
- xnb[j+XX*PACK_X8] = -NBAT_FAR_AWAY*(1 + cx);
- xnb[j+YY*PACK_X8] = -NBAT_FAR_AWAY*(1 + cy);
- xnb[j+ZZ*PACK_X8] = -NBAT_FAR_AWAY*(1 + cz + i);
- j++;
- c++;
- if (c == PACK_X8)
+ /* Complete the partially filled last cell with particles far apart */
+ for (; i < na_round; i++)
{
- j += (DIM-1)*PACK_X8;
- c = 0;
+ xnb[j++] = -NBAT_FAR_AWAY*(1 + cx);
+ xnb[j++] = -NBAT_FAR_AWAY*(1 + cy);
+ xnb[j++] = -NBAT_FAR_AWAY*(1 + cz + i);
+ j++;
}
- }
- break;
- default:
- gmx_incons("Unsupported stride");
+ break;
+ case nbatX4:
+ j = X4_IND_A(a0);
+ c = a0 & (PACK_X4-1);
+ for (i = 0; i < na; i++)
+ {
+ xnb[j+XX*PACK_X4] = x[a[i]][XX];
+ xnb[j+YY*PACK_X4] = x[a[i]][YY];
+ xnb[j+ZZ*PACK_X4] = x[a[i]][ZZ];
+ j++;
+ c++;
+ if (c == PACK_X4)
+ {
+ j += (DIM-1)*PACK_X4;
+ c = 0;
+ }
+ }
+ /* Complete the partially filled last cell with particles far apart */
+ for (; i < na_round; i++)
+ {
+ xnb[j+XX*PACK_X4] = -NBAT_FAR_AWAY*(1 + cx);
+ xnb[j+YY*PACK_X4] = -NBAT_FAR_AWAY*(1 + cy);
+ xnb[j+ZZ*PACK_X4] = -NBAT_FAR_AWAY*(1 + cz + i);
+ j++;
+ c++;
+ if (c == PACK_X4)
+ {
+ j += (DIM-1)*PACK_X4;
+ c = 0;
+ }
+ }
+ break;
+ case nbatX8:
+ j = X8_IND_A(a0);
+ c = a0 & (PACK_X8 - 1);
+ for (i = 0; i < na; i++)
+ {
+ xnb[j+XX*PACK_X8] = x[a[i]][XX];
+ xnb[j+YY*PACK_X8] = x[a[i]][YY];
+ xnb[j+ZZ*PACK_X8] = x[a[i]][ZZ];
+ j++;
+ c++;
+ if (c == PACK_X8)
+ {
+ j += (DIM-1)*PACK_X8;
+ c = 0;
+ }
+ }
+ /* Complete the partially filled last cell with particles far apart */
+ for (; i < na_round; i++)
+ {
+ xnb[j+XX*PACK_X8] = -NBAT_FAR_AWAY*(1 + cx);
+ xnb[j+YY*PACK_X8] = -NBAT_FAR_AWAY*(1 + cy);
+ xnb[j+ZZ*PACK_X8] = -NBAT_FAR_AWAY*(1 + cz + i);
+ j++;
+ c++;
+ if (c == PACK_X8)
+ {
+ j += (DIM-1)*PACK_X8;
+ c = 0;
+ }
+ }
+ break;
+ default:
+ gmx_incons("Unsupported stride");
}
}
*/
static void set_combination_rule_data(nbnxn_atomdata_t *nbat)
{
- int nt,i,j;
- real c6,c12;
+ int nt, i, j;
+ real c6, c12;
nt = nbat->ntype;
switch (nbat->comb_rule)
{
- case ljcrGEOM:
- nbat->comb_rule = ljcrGEOM;
+ case ljcrGEOM:
+ nbat->comb_rule = ljcrGEOM;
- for(i=0; i<nt; i++)
- {
- /* Copy the diagonal from the nbfp matrix */
- nbat->nbfp_comb[i*2 ] = sqrt(nbat->nbfp[(i*nt+i)*2 ]);
- nbat->nbfp_comb[i*2+1] = sqrt(nbat->nbfp[(i*nt+i)*2+1]);
- }
- break;
- case ljcrLB:
- for(i=0; i<nt; i++)
- {
- /* Get 6*C6 and 12*C12 from the diagonal of the nbfp matrix */
- c6 = nbat->nbfp[(i*nt+i)*2 ];
- c12 = nbat->nbfp[(i*nt+i)*2+1];
- if (c6 > 0 && c12 > 0)
+ for (i = 0; i < nt; i++)
{
- /* We store 0.5*2^1/6*sigma and sqrt(4*3*eps),
- * so we get 6*C6 and 12*C12 after combining.
- */
- nbat->nbfp_comb[i*2 ] = 0.5*pow(c12/c6,1.0/6.0);
- nbat->nbfp_comb[i*2+1] = sqrt(c6*c6/c12);
+ /* Copy the diagonal from the nbfp matrix */
+ nbat->nbfp_comb[i*2 ] = sqrt(nbat->nbfp[(i*nt+i)*2 ]);
+ nbat->nbfp_comb[i*2+1] = sqrt(nbat->nbfp[(i*nt+i)*2+1]);
}
- else
+ break;
+ case ljcrLB:
+ for (i = 0; i < nt; i++)
{
- nbat->nbfp_comb[i*2 ] = 0;
- nbat->nbfp_comb[i*2+1] = 0;
+ /* Get 6*C6 and 12*C12 from the diagonal of the nbfp matrix */
+ c6 = nbat->nbfp[(i*nt+i)*2 ];
+ c12 = nbat->nbfp[(i*nt+i)*2+1];
+ if (c6 > 0 && c12 > 0)
+ {
+ /* We store 0.5*2^1/6*sigma and sqrt(4*3*eps),
+ * so we get 6*C6 and 12*C12 after combining.
+ */
+ nbat->nbfp_comb[i*2 ] = 0.5*pow(c12/c6, 1.0/6.0);
+ nbat->nbfp_comb[i*2+1] = sqrt(c6*c6/c12);
+ }
+ else
+ {
+ nbat->nbfp_comb[i*2 ] = 0;
+ nbat->nbfp_comb[i*2+1] = 0;
+ }
}
- }
- break;
- case ljcrNONE:
- /* In nbfp_s4 we use a stride of 4 for storing two parameters */
- nbat->alloc((void **)&nbat->nbfp_s4,nt*nt*4*sizeof(*nbat->nbfp_s4));
- for(i=0; i<nt; i++)
- {
- for(j=0; j<nt; j++)
+ break;
+ case ljcrNONE:
+ /* In nbfp_s4 we use a stride of 4 for storing two parameters */
+ nbat->alloc((void **)&nbat->nbfp_s4, nt*nt*4*sizeof(*nbat->nbfp_s4));
+ for (i = 0; i < nt; i++)
{
- nbat->nbfp_s4[(i*nt+j)*4+0] = nbat->nbfp[(i*nt+j)*2+0];
- nbat->nbfp_s4[(i*nt+j)*4+1] = nbat->nbfp[(i*nt+j)*2+1];
- nbat->nbfp_s4[(i*nt+j)*4+2] = 0;
- nbat->nbfp_s4[(i*nt+j)*4+3] = 0;
+ for (j = 0; j < nt; j++)
+ {
+ nbat->nbfp_s4[(i*nt+j)*4+0] = nbat->nbfp[(i*nt+j)*2+0];
+ nbat->nbfp_s4[(i*nt+j)*4+1] = nbat->nbfp[(i*nt+j)*2+1];
+ nbat->nbfp_s4[(i*nt+j)*4+2] = 0;
+ nbat->nbfp_s4[(i*nt+j)*4+3] = 0;
+ }
}
- }
- break;
- default:
- gmx_incons("Unknown combination rule");
- break;
+ break;
+ default:
+ gmx_incons("Unknown combination rule");
+ break;
}
}
void nbnxn_atomdata_init(FILE *fp,
nbnxn_atomdata_t *nbat,
int nb_kernel_type,
- int ntype,const real *nbfp,
+ int ntype, const real *nbfp,
int n_energygroups,
int nout,
nbnxn_alloc_t *alloc,
nbnxn_free_t *free)
{
- int i,j;
- real c6,c12,tol;
- char *ptr;
- gmx_bool simple,bCombGeom,bCombLB;
+ int i, j;
+ real c6, c12, tol;
+ char *ptr;
+ gmx_bool simple, bCombGeom, bCombLB;
if (alloc == NULL)
{
if (debug)
{
- fprintf(debug,"There are %d atom types in the system, adding one for nbnxn_atomdata_t\n",ntype);
+ fprintf(debug, "There are %d atom types in the system, adding one for nbnxn_atomdata_t\n", ntype);
}
nbat->ntype = ntype + 1;
nbat->alloc((void **)&nbat->nbfp,
nbat->ntype*nbat->ntype*2*sizeof(*nbat->nbfp));
- nbat->alloc((void **)&nbat->nbfp_comb,nbat->ntype*2*sizeof(*nbat->nbfp_comb));
+ nbat->alloc((void **)&nbat->nbfp_comb, nbat->ntype*2*sizeof(*nbat->nbfp_comb));
/* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
* force-field floating point parameters.
{
double dbl;
- sscanf(ptr,"%lf",&dbl);
+ sscanf(ptr, "%lf", &dbl);
tol = dbl;
}
bCombGeom = TRUE;
/* Temporarily fill nbat->nbfp_comb with sigma and epsilon
* to check for the LB rule.
*/
- for(i=0; i<ntype; i++)
+ for (i = 0; i < ntype; i++)
{
c6 = nbfp[(i*ntype+i)*2 ]/6.0;
c12 = nbfp[(i*ntype+i)*2+1]/12.0;
if (c6 > 0 && c12 > 0)
{
- nbat->nbfp_comb[i*2 ] = pow(c12/c6,1.0/6.0);
+ nbat->nbfp_comb[i*2 ] = pow(c12/c6, 1.0/6.0);
nbat->nbfp_comb[i*2+1] = 0.25*c6*c6/c12;
}
else if (c6 == 0 && c12 == 0)
}
}
- for(i=0; i<nbat->ntype; i++)
+ for (i = 0; i < nbat->ntype; i++)
{
- for(j=0; j<nbat->ntype; j++)
+ for (j = 0; j < nbat->ntype; j++)
{
if (i < ntype && j < ntype)
{
/* Compare 6*C6 and 12*C12 for geometric cobination rule */
bCombGeom = bCombGeom &&
- gmx_within_tol(c6*c6 ,nbfp[(i*ntype+i)*2 ]*nbfp[(j*ntype+j)*2 ],tol) &&
- gmx_within_tol(c12*c12,nbfp[(i*ntype+i)*2+1]*nbfp[(j*ntype+j)*2+1],tol);
+ gmx_within_tol(c6*c6, nbfp[(i*ntype+i)*2 ]*nbfp[(j*ntype+j)*2 ], tol) &&
+ gmx_within_tol(c12*c12, nbfp[(i*ntype+i)*2+1]*nbfp[(j*ntype+j)*2+1], tol);
/* Compare C6 and C12 for Lorentz-Berthelot combination rule */
- c6 /= 6.0;
- c12 /= 12.0;
+ c6 /= 6.0;
+ c12 /= 12.0;
bCombLB = bCombLB &&
((c6 == 0 && c12 == 0 &&
(nbat->nbfp_comb[i*2+1] == 0 || nbat->nbfp_comb[j*2+1] == 0)) ||
(c6 > 0 && c12 > 0 &&
- gmx_within_tol(pow(c12/c6,1.0/6.0),0.5*(nbat->nbfp_comb[i*2]+nbat->nbfp_comb[j*2]),tol) &&
- gmx_within_tol(0.25*c6*c6/c12,sqrt(nbat->nbfp_comb[i*2+1]*nbat->nbfp_comb[j*2+1]),tol)));
+ gmx_within_tol(pow(c12/c6, 1.0/6.0), 0.5*(nbat->nbfp_comb[i*2]+nbat->nbfp_comb[j*2]), tol) &&
+ gmx_within_tol(0.25*c6*c6/c12, sqrt(nbat->nbfp_comb[i*2+1]*nbat->nbfp_comb[j*2+1]), tol)));
}
else
{
}
if (debug)
{
- fprintf(debug,"Combination rules: geometric %d Lorentz-Berthelot %d\n",
- bCombGeom,bCombLB);
+ fprintf(debug, "Combination rules: geometric %d Lorentz-Berthelot %d\n",
+ bCombGeom, bCombLB);
}
simple = nbnxn_kernel_pairlist_simple(nb_kernel_type);
{
if (nbat->comb_rule == ljcrNONE)
{
- fprintf(fp,"Using full Lennard-Jones parameter combination matrix\n\n");
+ fprintf(fp, "Using full Lennard-Jones parameter combination matrix\n\n");
}
else
{
- fprintf(fp,"Using %s Lennard-Jones combination rule\n\n",
- nbat->comb_rule==ljcrGEOM ? "geometric" : "Lorentz-Berthelot");
+ fprintf(fp, "Using %s Lennard-Jones combination rule\n\n",
+ nbat->comb_rule == ljcrGEOM ? "geometric" : "Lorentz-Berthelot");
}
}
switch (nb_kernel_type)
{
- case nbnxnk4xN_SIMD_4xN:
- case nbnxnk4xN_SIMD_2xNN:
- pack_x = max(NBNXN_CPU_CLUSTER_I_SIZE,
- nbnxn_kernel_to_cj_size(nb_kernel_type));
- switch (pack_x)
- {
- case 4:
- nbat->XFormat = nbatX4;
- break;
- case 8:
- nbat->XFormat = nbatX8;
- break;
- default:
- gmx_incons("Unsupported packing width");
- }
- break;
- default:
- nbat->XFormat = nbatXYZ;
- break;
+ case nbnxnk4xN_SIMD_4xN:
+ case nbnxnk4xN_SIMD_2xNN:
+ pack_x = max(NBNXN_CPU_CLUSTER_I_SIZE,
+ nbnxn_kernel_to_cj_size(nb_kernel_type));
+ switch (pack_x)
+ {
+ case 4:
+ nbat->XFormat = nbatX4;
+ break;
+ case 8:
+ nbat->XFormat = nbatX8;
+ break;
+ default:
+ gmx_incons("Unsupported packing width");
+ }
+ break;
+ default:
+ nbat->XFormat = nbatXYZ;
+ break;
}
nbat->FFormat = nbat->XFormat;
nbat->XFormat = nbatXYZQ;
nbat->FFormat = nbatXYZ;
}
- nbat->q = NULL;
+ nbat->q = NULL;
nbat->nenergrp = n_energygroups;
if (!simple)
{
/* Energy groups not supported yet for super-sub lists */
if (n_energygroups > 1 && fp != NULL)
{
- fprintf(fp,"\nNOTE: With GPUs, reporting energy group contributions is not supported\n\n");
+ fprintf(fp, "\nNOTE: With GPUs, reporting energy group contributions is not supported\n\n");
}
nbat->nenergrp = 1;
}
/* Temporary storage goes as #grp^3*simd_width^2/2, so limit to 64 */
if (nbat->nenergrp > 64)
{
- gmx_fatal(FARGS,"With NxN kernels not more than 64 energy groups are supported\n");
+ gmx_fatal(FARGS, "With NxN kernels not more than 64 energy groups are supported\n");
}
nbat->neg_2log = 1;
while (nbat->nenergrp > (1<<nbat->neg_2log))
nbat->neg_2log++;
}
nbat->energrp = NULL;
- nbat->alloc((void **)&nbat->shift_vec,SHIFTS*sizeof(*nbat->shift_vec));
+ nbat->alloc((void **)&nbat->shift_vec, SHIFTS*sizeof(*nbat->shift_vec));
nbat->xstride = (nbat->XFormat == nbatXYZQ ? STRIDE_XYZQ : DIM);
nbat->fstride = (nbat->FFormat == nbatXYZQ ? STRIDE_XYZQ : DIM);
nbat->x = NULL;
* we substract 0.5 to avoid rounding issues.
* In the kernel we can subtract 1 to generate the subsequent mask.
*/
- const int simd_width=GMX_NBNXN_SIMD_BITWIDTH/(sizeof(real)*8);
- int simd_4xn_diag_size,j;
+ const int simd_width = GMX_NBNXN_SIMD_BITWIDTH/(sizeof(real)*8);
+ int simd_4xn_diag_size, j;
- simd_4xn_diag_size = max(NBNXN_CPU_CLUSTER_I_SIZE,simd_width);
- snew_aligned(nbat->simd_4xn_diag,simd_4xn_diag_size,NBNXN_MEM_ALIGN);
- for(j=0; j<simd_4xn_diag_size; j++)
+ simd_4xn_diag_size = max(NBNXN_CPU_CLUSTER_I_SIZE, simd_width);
+ snew_aligned(nbat->simd_4xn_diag, simd_4xn_diag_size, NBNXN_MEM_ALIGN);
+ for (j = 0; j < simd_4xn_diag_size; j++)
{
nbat->simd_4xn_diag[j] = j - 0.5;
}
- snew_aligned(nbat->simd_2xnn_diag,simd_width,NBNXN_MEM_ALIGN);
- for(j=0; j<simd_width/2; j++)
+ snew_aligned(nbat->simd_2xnn_diag, simd_width, NBNXN_MEM_ALIGN);
+ for (j = 0; j < simd_width/2; j++)
{
/* The j-cluster size is half the SIMD width */
nbat->simd_2xnn_diag[j] = j - 0.5;
/* Initialize the output data structures */
nbat->nout = nout;
- snew(nbat->out,nbat->nout);
+ snew(nbat->out, nbat->nout);
nbat->nalloc = 0;
- for(i=0; i<nbat->nout; i++)
+ for (i = 0; i < nbat->nout; i++)
{
nbnxn_atomdata_output_init(&nbat->out[i],
nb_kernel_type,
- nbat->nenergrp,1<<nbat->neg_2log,
+ nbat->nenergrp, 1<<nbat->neg_2log,
nbat->alloc);
}
nbat->buffer_flags.flag = NULL;
}
static void copy_lj_to_nbat_lj_comb_x4(const real *ljparam_type,
- const int *type,int na,
+ const int *type, int na,
real *ljparam_at)
{
- int is,k,i;
+ int is, k, i;
/* The LJ params follow the combination rule:
* copy the params for the type array to the atom array.
*/
- for(is=0; is<na; is+=PACK_X4)
+ for (is = 0; is < na; is += PACK_X4)
{
- for(k=0; k<PACK_X4; k++)
+ for (k = 0; k < PACK_X4; k++)
{
i = is + k;
ljparam_at[is*2 +k] = ljparam_type[type[i]*2 ];
}
static void copy_lj_to_nbat_lj_comb_x8(const real *ljparam_type,
- const int *type,int na,
+ const int *type, int na,
real *ljparam_at)
{
- int is,k,i;
+ int is, k, i;
/* The LJ params follow the combination rule:
* copy the params for the type array to the atom array.
*/
- for(is=0; is<na; is+=PACK_X8)
+ for (is = 0; is < na; is += PACK_X8)
{
- for(k=0; k<PACK_X8; k++)
+ for (k = 0; k < PACK_X8; k++)
{
i = is + k;
ljparam_at[is*2 +k] = ljparam_type[type[i]*2 ];
}
/* Sets the atom type and LJ data in nbnxn_atomdata_t */
-static void nbnxn_atomdata_set_atomtypes(nbnxn_atomdata_t *nbat,
- int ngrid,
+static void nbnxn_atomdata_set_atomtypes(nbnxn_atomdata_t *nbat,
+ int ngrid,
const nbnxn_search_t nbs,
- const int *type)
+ const int *type)
{
- int g,i,ncz,ash;
+ int g, i, ncz, ash;
const nbnxn_grid_t *grid;
- for(g=0; g<ngrid; g++)
+ for (g = 0; g < ngrid; g++)
{
grid = &nbs->grid[g];
/* Loop over all columns and copy and fill */
- for(i=0; i<grid->ncx*grid->ncy; i++)
+ for (i = 0; i < grid->ncx*grid->ncy; i++)
{
ncz = grid->cxy_ind[i+1] - grid->cxy_ind[i];
ash = (grid->cell0 + grid->cxy_ind[i])*grid->na_sc;
- copy_int_to_nbat_int(nbs->a+ash,grid->cxy_na[i],ncz*grid->na_sc,
- type,nbat->ntype-1,nbat->type+ash);
+ copy_int_to_nbat_int(nbs->a+ash, grid->cxy_na[i], ncz*grid->na_sc,
+ type, nbat->ntype-1, nbat->type+ash);
if (nbat->comb_rule != ljcrNONE)
{
if (nbat->XFormat == nbatX4)
{
copy_lj_to_nbat_lj_comb_x4(nbat->nbfp_comb,
- nbat->type+ash,ncz*grid->na_sc,
+ nbat->type+ash, ncz*grid->na_sc,
nbat->lj_comb+ash*2);
}
else if (nbat->XFormat == nbatX8)
{
copy_lj_to_nbat_lj_comb_x8(nbat->nbfp_comb,
- nbat->type+ash,ncz*grid->na_sc,
+ nbat->type+ash, ncz*grid->na_sc,
nbat->lj_comb+ash*2);
}
}
}
/* Sets the charges in nbnxn_atomdata_t *nbat */
-static void nbnxn_atomdata_set_charges(nbnxn_atomdata_t *nbat,
- int ngrid,
+static void nbnxn_atomdata_set_charges(nbnxn_atomdata_t *nbat,
+ int ngrid,
const nbnxn_search_t nbs,
- const real *charge)
+ const real *charge)
{
- int g,cxy,ncz,ash,na,na_round,i,j;
- real *q;
+ int g, cxy, ncz, ash, na, na_round, i, j;
+ real *q;
const nbnxn_grid_t *grid;
- for(g=0; g<ngrid; g++)
+ for (g = 0; g < ngrid; g++)
{
grid = &nbs->grid[g];
/* Loop over all columns and copy and fill */
- for(cxy=0; cxy<grid->ncx*grid->ncy; cxy++)
+ for (cxy = 0; cxy < grid->ncx*grid->ncy; cxy++)
{
- ash = (grid->cell0 + grid->cxy_ind[cxy])*grid->na_sc;
- na = grid->cxy_na[cxy];
+ ash = (grid->cell0 + grid->cxy_ind[cxy])*grid->na_sc;
+ na = grid->cxy_na[cxy];
na_round = (grid->cxy_ind[cxy+1] - grid->cxy_ind[cxy])*grid->na_sc;
if (nbat->XFormat == nbatXYZQ)
{
q = nbat->x + ash*STRIDE_XYZQ + ZZ + 1;
- for(i=0; i<na; i++)
+ for (i = 0; i < na; i++)
{
*q = charge[nbs->a[ash+i]];
q += STRIDE_XYZQ;
}
/* Complete the partially filled last cell with zeros */
- for(; i<na_round; i++)
+ for (; i < na_round; i++)
{
*q = 0;
q += STRIDE_XYZQ;
else
{
q = nbat->q + ash;
- for(i=0; i<na; i++)
+ for (i = 0; i < na; i++)
{
*q = charge[nbs->a[ash+i]];
q++;
}
/* Complete the partially filled last cell with zeros */
- for(; i<na_round; i++)
+ for (; i < na_round; i++)
{
*q = 0;
q++;
}
/* Copies the energy group indices to a reordered and packed array */
-static void copy_egp_to_nbat_egps(const int *a,int na,int na_round,
- int na_c,int bit_shift,
- const int *in,int *innb)
+static void copy_egp_to_nbat_egps(const int *a, int na, int na_round,
+ int na_c, int bit_shift,
+ const int *in, int *innb)
{
- int i,j,sa,at;
+ int i, j, sa, at;
int comb;
j = 0;
- for(i=0; i<na; i+=na_c)
+ for (i = 0; i < na; i += na_c)
{
/* Store na_c energy group numbers into one int */
comb = 0;
- for(sa=0; sa<na_c; sa++)
+ for (sa = 0; sa < na_c; sa++)
{
at = a[i+sa];
if (at >= 0)
innb[j++] = comb;
}
/* Complete the partially filled last cell with fill */
- for(; i<na_round; i+=na_c)
+ for (; i < na_round; i += na_c)
{
innb[j++] = 0;
}
}
/* Set the energy group indices for atoms in nbnxn_atomdata_t */
-static void nbnxn_atomdata_set_energygroups(nbnxn_atomdata_t *nbat,
- int ngrid,
+static void nbnxn_atomdata_set_energygroups(nbnxn_atomdata_t *nbat,
+ int ngrid,
const nbnxn_search_t nbs,
- const int *atinfo)
+ const int *atinfo)
{
- int g,i,ncz,ash;
+ int g, i, ncz, ash;
const nbnxn_grid_t *grid;
- for(g=0; g<ngrid; g++)
+ for (g = 0; g < ngrid; g++)
{
grid = &nbs->grid[g];
/* Loop over all columns and copy and fill */
- for(i=0; i<grid->ncx*grid->ncy; i++)
+ for (i = 0; i < grid->ncx*grid->ncy; i++)
{
ncz = grid->cxy_ind[i+1] - grid->cxy_ind[i];
ash = (grid->cell0 + grid->cxy_ind[i])*grid->na_sc;
- copy_egp_to_nbat_egps(nbs->a+ash,grid->cxy_na[i],ncz*grid->na_sc,
- nbat->na_c,nbat->neg_2log,
- atinfo,nbat->energrp+(ash>>grid->na_c_2log));
+ copy_egp_to_nbat_egps(nbs->a+ash, grid->cxy_na[i], ncz*grid->na_sc,
+ nbat->na_c, nbat->neg_2log,
+ atinfo, nbat->energrp+(ash>>grid->na_c_2log));
}
}
}
/* Sets all required atom parameter data in nbnxn_atomdata_t */
-void nbnxn_atomdata_set(nbnxn_atomdata_t *nbat,
- int locality,
+void nbnxn_atomdata_set(nbnxn_atomdata_t *nbat,
+ int locality,
const nbnxn_search_t nbs,
- const t_mdatoms *mdatoms,
- const int *atinfo)
+ const t_mdatoms *mdatoms,
+ const int *atinfo)
{
int ngrid;
ngrid = nbs->ngrid;
}
- nbnxn_atomdata_set_atomtypes(nbat,ngrid,nbs,mdatoms->typeA);
+ nbnxn_atomdata_set_atomtypes(nbat, ngrid, nbs, mdatoms->typeA);
- nbnxn_atomdata_set_charges(nbat,ngrid,nbs,mdatoms->chargeA);
+ nbnxn_atomdata_set_charges(nbat, ngrid, nbs, mdatoms->chargeA);
if (nbat->nenergrp > 1)
{
- nbnxn_atomdata_set_energygroups(nbat,ngrid,nbs,atinfo);
+ nbnxn_atomdata_set_energygroups(nbat, ngrid, nbs, atinfo);
}
}
/* Copies the shift vector array to nbnxn_atomdata_t */
-void nbnxn_atomdata_copy_shiftvec(gmx_bool bDynamicBox,
- rvec *shift_vec,
- nbnxn_atomdata_t *nbat)
+void nbnxn_atomdata_copy_shiftvec(gmx_bool bDynamicBox,
+ rvec *shift_vec,
+ nbnxn_atomdata_t *nbat)
{
int i;
nbat->bDynamicBox = bDynamicBox;
- for(i=0; i<SHIFTS; i++)
+ for (i = 0; i < SHIFTS; i++)
{
- copy_rvec(shift_vec[i],nbat->shift_vec[i]);
+ copy_rvec(shift_vec[i], nbat->shift_vec[i]);
}
}
/* Copies (and reorders) the coordinates to nbnxn_atomdata_t */
void nbnxn_atomdata_copy_x_to_nbat_x(const nbnxn_search_t nbs,
- int locality,
- gmx_bool FillLocal,
- rvec *x,
- nbnxn_atomdata_t *nbat)
+ int locality,
+ gmx_bool FillLocal,
+ rvec *x,
+ nbnxn_atomdata_t *nbat)
{
- int g0=0,g1=0;
- int nth,th;
+ int g0 = 0, g1 = 0;
+ int nth, th;
switch (locality)
{
- case eatAll:
- g0 = 0;
- g1 = nbs->ngrid;
- break;
- case eatLocal:
- g0 = 0;
- g1 = 1;
- break;
- case eatNonlocal:
- g0 = 1;
- g1 = nbs->ngrid;
- break;
+ case eatAll:
+ g0 = 0;
+ g1 = nbs->ngrid;
+ break;
+ case eatLocal:
+ g0 = 0;
+ g1 = 1;
+ break;
+ case eatNonlocal:
+ g0 = 1;
+ g1 = nbs->ngrid;
+ break;
}
if (FillLocal)
nth = gmx_omp_nthreads_get(emntPairsearch);
#pragma omp parallel for num_threads(nth) schedule(static)
- for(th=0; th<nth; th++)
+ for (th = 0; th < nth; th++)
{
int g;
- for(g=g0; g<g1; g++)
+ for (g = g0; g < g1; g++)
{
const nbnxn_grid_t *grid;
- int cxy0,cxy1,cxy;
+ int cxy0, cxy1, cxy;
grid = &nbs->grid[g];
cxy0 = (grid->ncx*grid->ncy* th +nth-1)/nth;
cxy1 = (grid->ncx*grid->ncy*(th+1)+nth-1)/nth;
- for(cxy=cxy0; cxy<cxy1; cxy++)
+ for (cxy = cxy0; cxy < cxy1; cxy++)
{
- int na,ash,na_fill;
+ int na, ash, na_fill;
na = grid->cxy_na[cxy];
ash = (grid->cell0 + grid->cxy_ind[cxy])*grid->na_sc;
*/
na_fill = na;
}
- copy_rvec_to_nbat_real(nbs->a+ash,na,na_fill,x,
- nbat->XFormat,nbat->x,ash,
- 0,0,0);
+ copy_rvec_to_nbat_real(nbs->a+ash, na, na_fill, x,
+ nbat->XFormat, nbat->x, ash,
+ 0, 0, 0);
}
}
}
{
int i;
- for(i=i0; i<i1; i++)
+ for (i = i0; i < i1; i++)
{
dest[i] = 0;
}
int nsrc,
int i0, int i1)
{
- int i,s;
+ int i, s;
if (bDestSet)
{
/* The destination buffer contains data, add to it */
- for(i=i0; i<i1; i++)
+ for (i = i0; i < i1; i++)
{
- for(s=0; s<nsrc; s++)
+ for (s = 0; s < nsrc; s++)
{
dest[i] += src[s][i];
}
else
{
/* The destination buffer is unitialized, set it first */
- for(i=i0; i<i1; i++)
+ for (i = i0; i < i1; i++)
{
dest[i] = src[0][i];
- for(s=1; s<nsrc; s++)
+ for (s = 1; s < nsrc; s++)
{
dest[i] += src[s][i];
}
#endif
#include "gmx_simd_macros.h"
- int i,s;
- gmx_mm_pr dest_SSE,src_SSE;
+ int i, s;
+ gmx_mm_pr dest_SSE, src_SSE;
if (bDestSet)
{
- for(i=i0; i<i1; i+=GMX_SIMD_WIDTH_HERE)
+ for (i = i0; i < i1; i += GMX_SIMD_WIDTH_HERE)
{
dest_SSE = gmx_load_pr(dest+i);
- for(s=0; s<nsrc; s++)
+ for (s = 0; s < nsrc; s++)
{
src_SSE = gmx_load_pr(src[s]+i);
- dest_SSE = gmx_add_pr(dest_SSE,src_SSE);
+ dest_SSE = gmx_add_pr(dest_SSE, src_SSE);
}
- gmx_store_pr(dest+i,dest_SSE);
+ gmx_store_pr(dest+i, dest_SSE);
}
}
else
{
- for(i=i0; i<i1; i+=GMX_SIMD_WIDTH_HERE)
+ for (i = i0; i < i1; i += GMX_SIMD_WIDTH_HERE)
{
dest_SSE = gmx_load_pr(src[0]+i);
- for(s=1; s<nsrc; s++)
+ for (s = 1; s < nsrc; s++)
{
src_SSE = gmx_load_pr(src[s]+i);
- dest_SSE = gmx_add_pr(dest_SSE,src_SSE);
+ dest_SSE = gmx_add_pr(dest_SSE, src_SSE);
}
- gmx_store_pr(dest+i,dest_SSE);
+ gmx_store_pr(dest+i, dest_SSE);
}
}
const nbnxn_atomdata_t *nbat,
nbnxn_atomdata_output_t *out,
int nfa,
- int a0,int a1,
+ int a0, int a1,
rvec *f)
{
- int a,i,fa;
+ int a, i, fa;
const int *cell;
const real *fnb;
/* Loop over all columns and copy and fill */
switch (nbat->FFormat)
{
- case nbatXYZ:
- case nbatXYZQ:
- if (nfa == 1)
- {
- fnb = out[0].f;
-
- for(a=a0; a<a1; a++)
+ case nbatXYZ:
+ case nbatXYZQ:
+ if (nfa == 1)
{
- i = cell[a]*nbat->fstride;
+ fnb = out[0].f;
- f[a][XX] += fnb[i];
- f[a][YY] += fnb[i+1];
- f[a][ZZ] += fnb[i+2];
+ for (a = a0; a < a1; a++)
+ {
+ i = cell[a]*nbat->fstride;
+
+ f[a][XX] += fnb[i];
+ f[a][YY] += fnb[i+1];
+ f[a][ZZ] += fnb[i+2];
+ }
}
- }
- else
- {
- for(a=a0; a<a1; a++)
+ else
{
- i = cell[a]*nbat->fstride;
-
- for(fa=0; fa<nfa; fa++)
+ for (a = a0; a < a1; a++)
{
- f[a][XX] += out[fa].f[i];
- f[a][YY] += out[fa].f[i+1];
- f[a][ZZ] += out[fa].f[i+2];
+ i = cell[a]*nbat->fstride;
+
+ for (fa = 0; fa < nfa; fa++)
+ {
+ f[a][XX] += out[fa].f[i];
+ f[a][YY] += out[fa].f[i+1];
+ f[a][ZZ] += out[fa].f[i+2];
+ }
}
}
- }
- break;
- case nbatX4:
- if (nfa == 1)
- {
- fnb = out[0].f;
-
- for(a=a0; a<a1; a++)
+ break;
+ case nbatX4:
+ if (nfa == 1)
{
- i = X4_IND_A(cell[a]);
+ fnb = out[0].f;
+
+ for (a = a0; a < a1; a++)
+ {
+ i = X4_IND_A(cell[a]);
- f[a][XX] += fnb[i+XX*PACK_X4];
- f[a][YY] += fnb[i+YY*PACK_X4];
- f[a][ZZ] += fnb[i+ZZ*PACK_X4];
+ f[a][XX] += fnb[i+XX*PACK_X4];
+ f[a][YY] += fnb[i+YY*PACK_X4];
+ f[a][ZZ] += fnb[i+ZZ*PACK_X4];
+ }
}
- }
- else
- {
- for(a=a0; a<a1; a++)
+ else
{
- i = X4_IND_A(cell[a]);
-
- for(fa=0; fa<nfa; fa++)
+ for (a = a0; a < a1; a++)
{
- f[a][XX] += out[fa].f[i+XX*PACK_X4];
- f[a][YY] += out[fa].f[i+YY*PACK_X4];
- f[a][ZZ] += out[fa].f[i+ZZ*PACK_X4];
+ i = X4_IND_A(cell[a]);
+
+ for (fa = 0; fa < nfa; fa++)
+ {
+ f[a][XX] += out[fa].f[i+XX*PACK_X4];
+ f[a][YY] += out[fa].f[i+YY*PACK_X4];
+ f[a][ZZ] += out[fa].f[i+ZZ*PACK_X4];
+ }
}
}
- }
- break;
- case nbatX8:
- if (nfa == 1)
- {
- fnb = out[0].f;
-
- for(a=a0; a<a1; a++)
+ break;
+ case nbatX8:
+ if (nfa == 1)
{
- i = X8_IND_A(cell[a]);
+ fnb = out[0].f;
- f[a][XX] += fnb[i+XX*PACK_X8];
- f[a][YY] += fnb[i+YY*PACK_X8];
- f[a][ZZ] += fnb[i+ZZ*PACK_X8];
+ for (a = a0; a < a1; a++)
+ {
+ i = X8_IND_A(cell[a]);
+
+ f[a][XX] += fnb[i+XX*PACK_X8];
+ f[a][YY] += fnb[i+YY*PACK_X8];
+ f[a][ZZ] += fnb[i+ZZ*PACK_X8];
+ }
}
- }
- else
- {
- for(a=a0; a<a1; a++)
+ else
{
- i = X8_IND_A(cell[a]);
-
- for(fa=0; fa<nfa; fa++)
+ for (a = a0; a < a1; a++)
{
- f[a][XX] += out[fa].f[i+XX*PACK_X8];
- f[a][YY] += out[fa].f[i+YY*PACK_X8];
- f[a][ZZ] += out[fa].f[i+ZZ*PACK_X8];
+ i = X8_IND_A(cell[a]);
+
+ for (fa = 0; fa < nfa; fa++)
+ {
+ f[a][XX] += out[fa].f[i+XX*PACK_X8];
+ f[a][YY] += out[fa].f[i+YY*PACK_X8];
+ f[a][ZZ] += out[fa].f[i+ZZ*PACK_X8];
+ }
}
}
- }
- break;
+ break;
}
}
/* Add the force array(s) from nbnxn_atomdata_t to f */
-void nbnxn_atomdata_add_nbat_f_to_f(const nbnxn_search_t nbs,
- int locality,
+void nbnxn_atomdata_add_nbat_f_to_f(const nbnxn_search_t nbs,
+ int locality,
const nbnxn_atomdata_t *nbat,
- rvec *f)
+ rvec *f)
{
- int a0=0,na=0;
- int nth,th;
+ int a0 = 0, na = 0;
+ int nth, th;
nbs_cycle_start(&nbs->cc[enbsCCreducef]);
switch (locality)
{
- case eatAll:
- a0 = 0;
- na = nbs->natoms_nonlocal;
- break;
- case eatLocal:
- a0 = 0;
- na = nbs->natoms_local;
- break;
- case eatNonlocal:
- a0 = nbs->natoms_local;
- na = nbs->natoms_nonlocal - nbs->natoms_local;
- break;
+ case eatAll:
+ a0 = 0;
+ na = nbs->natoms_nonlocal;
+ break;
+ case eatLocal:
+ a0 = 0;
+ na = nbs->natoms_local;
+ break;
+ case eatNonlocal:
+ a0 = nbs->natoms_local;
+ na = nbs->natoms_nonlocal - nbs->natoms_local;
+ break;
}
nth = gmx_omp_nthreads_get(emntNonbonded);
* them to the, differently ordered, "real" force buffer.
*/
#pragma omp parallel for num_threads(nth) schedule(static)
- for(th=0; th<nth; th++)
+ for (th = 0; th < nth; th++)
{
const nbnxn_buffer_flags_t *flags;
- int b0,b1,b;
- int i0,i1;
- int nfptr;
+ int b0, b1, b;
+ int i0, i1;
+ int nfptr;
real *fptr[NBNXN_BUFFERFLAG_MAX_THREADS];
- int out;
+ int out;
flags = &nbat->buffer_flags;
b0 = (flags->nflag* th )/nth;
b1 = (flags->nflag*(th+1))/nth;
- for(b=b0; b<b1; b++)
+ for (b = b0; b < b1; b++)
{
i0 = b *NBNXN_BUFFERFLAG_SIZE*nbat->fstride;
i1 = (b+1)*NBNXN_BUFFERFLAG_SIZE*nbat->fstride;
nfptr = 0;
- for(out=1; out<nbat->nout; out++)
+ for (out = 1; out < nbat->nout; out++)
{
if (flags->flag[b] & (1U<<out))
{
#else
nbnxn_atomdata_reduce_reals
#endif
- (nbat->out[0].f,
- flags->flag[b] & (1U<<0),
- fptr,nfptr,
- i0,i1);
+ (nbat->out[0].f,
+ flags->flag[b] & (1U<<0),
+ fptr, nfptr,
+ i0, i1);
}
else if (!(flags->flag[b] & (1U<<0)))
{
nbnxn_atomdata_clear_reals(nbat->out[0].f,
- i0,i1);
+ i0, i1);
}
}
}
}
#pragma omp parallel for num_threads(nth) schedule(static)
- for(th=0; th<nth; th++)
+ for (th = 0; th < nth; th++)
{
- nbnxn_atomdata_add_nbat_f_to_f_part(nbs,nbat,
+ nbnxn_atomdata_add_nbat_f_to_f_part(nbs, nbat,
nbat->out,
1,
a0+((th+0)*na)/nth,
/* Adds the shift forces from nbnxn_atomdata_t to fshift */
void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t *nbat,
- rvec *fshift)
+ rvec *fshift)
{
const nbnxn_atomdata_output_t *out;
int th;
rvec sum;
out = nbat->out;
-
- for(s=0; s<SHIFTS; s++)
+
+ for (s = 0; s < SHIFTS; s++)
{
clear_rvec(sum);
- for(th=0; th<nbat->nout; th++)
+ for (th = 0; th < nbat->nout; th++)
{
sum[XX] += out[th].fshift[s*DIM+XX];
sum[YY] += out[th].fshift[s*DIM+YY];
sum[ZZ] += out[th].fshift[s*DIM+ZZ];
}
- rvec_inc(fshift[s],sum);
+ rvec_inc(fshift[s], sum);
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff