-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
- * This source code is part of
- *
- * G R O M A C S
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
*
- * GROningen MAchine for Chemical Simulations
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2012, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
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+ * You should have received a copy of the GNU Lesser General Public
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*
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+ * If you want to redistribute modifications to GROMACS, please
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+ * official version at http://www.gromacs.org.
*
* To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
- *
- * For more info, check our website at http://www.gromacs.org
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "nbnxn_atomdata.h"
+#include "config.h"
+
+#include <assert.h>
#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include "smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "nbnxn_consts.h"
-#include "nbnxn_internal.h"
-#include "nbnxn_search.h"
-#include "nbnxn_atomdata.h"
-#include "gmx_omp_nthreads.h"
-/* Default nbnxn allocation routine, allocates 32 byte aligned,
- * which works for plain C and aligned SSE and AVX loads/stores.
- */
-void nbnxn_alloc_aligned(void **ptr,size_t nbytes)
+#include "thread_mpi/atomic.h"
+
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_internal.h"
+#include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
+
+/* Default nbnxn allocation routine, allocates NBNXN_MEM_ALIGN byte aligned */
+void nbnxn_alloc_aligned(void **ptr, size_t nbytes)
{
- *ptr = save_malloc_aligned("ptr",__FILE__,__LINE__,nbytes,1,32);
+ *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 == nbk4xN_X86_SIMD128 ||
- nb_kernel_type == nbk4xN_X86_SIMD256)
+ 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 nbnxn_atomdata_t format");
}
}
-/* Determines the combination rule (or none) to be used, stores it,
- * and sets the LJ parameters required with the rule.
- */
-static void set_combination_rule_data(nbnxn_atomdata_t *nbat)
+/* Stores the LJ parameter data in a format convenient for different kernels */
+static void set_lj_parameter_data(nbnxn_atomdata_t *nbat, gmx_bool bSIMD)
{
- int nt,i,j;
- real c6,c12;
+ int nt, i, j;
+ real c6, c12;
nt = nbat->ntype;
- switch (nbat->comb_rule)
+ if (bSIMD)
{
- case ljcrGEOM:
- nbat->comb_rule = ljcrGEOM;
-
- for(i=0; i<nt; i++)
+ /* nbfp_s4 stores two parameters using a stride of 4,
+ * because this would suit x86 SIMD single-precision
+ * quad-load intrinsics. There's a slight inefficiency in
+ * allocating and initializing nbfp_s4 when it might not
+ * be used, but introducing the conditional code is not
+ * really worth it. */
+ nbat->alloc((void **)&nbat->nbfp_s4, nt*nt*4*sizeof(*nbat->nbfp_s4));
+ 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)
- {
- /* 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++)
+ 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+3] = 0;
}
}
- break;
- default:
- gmx_incons("Unknown combination rule");
- break;
}
+
+ /* We use combination rule data for SIMD combination rule kernels
+ * and with LJ-PME kernels. We then only need parameters per atom type,
+ * not per pair of atom types.
+ */
+ switch (nbat->comb_rule)
+ {
+ case ljcrGEOM:
+ nbat->comb_rule = ljcrGEOM;
+
+ for (i = 0; i < nt; i++)
+ {
+ /* Store the sqrt of 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)
+ {
+ /* 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:
+ /* We always store the full matrix (see code above) */
+ break;
+ default:
+ gmx_incons("Unknown combination rule");
+ break;
+ }
+}
+
+#ifdef GMX_NBNXN_SIMD
+static void
+nbnxn_atomdata_init_simple_exclusion_masks(nbnxn_atomdata_t *nbat)
+{
+ int i, j;
+ const int simd_width = GMX_SIMD_REAL_WIDTH;
+ int simd_excl_size;
+ /* Set the diagonal cluster pair exclusion mask setup data.
+ * In the kernel we check 0 < j - i to generate the masks.
+ * Here we store j - i for generating the mask for the first i,
+ * we substract 0.5 to avoid rounding issues.
+ * In the kernel we can subtract 1 to generate the subsequent mask.
+ */
+ int simd_4xn_diag_size;
+ const real simdFalse = -1, simdTrue = 1;
+ real *simd_interaction_array;
+
+ simd_4xn_diag_size = max(NBNXN_CPU_CLUSTER_I_SIZE, simd_width);
+ snew_aligned(nbat->simd_4xn_diagonal_j_minus_i, simd_4xn_diag_size, NBNXN_MEM_ALIGN);
+ for (j = 0; j < simd_4xn_diag_size; j++)
+ {
+ nbat->simd_4xn_diagonal_j_minus_i[j] = j - 0.5;
+ }
+
+ snew_aligned(nbat->simd_2xnn_diagonal_j_minus_i, 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_diagonal_j_minus_i[j] = j - 0.5;
+ /* The next half of the SIMD width is for i + 1 */
+ nbat->simd_2xnn_diagonal_j_minus_i[simd_width/2+j] = j - 1 - 0.5;
+ }
+
+ /* We use up to 32 bits for exclusion masking.
+ * The same masks are used for the 4xN and 2x(N+N) kernels.
+ * The masks are read either into epi32 SIMD registers or into
+ * real SIMD registers (together with a cast).
+ * In single precision this means the real and epi32 SIMD registers
+ * are of equal size.
+ * In double precision the epi32 registers can be smaller than
+ * the real registers, so depending on the architecture, we might
+ * need to use two, identical, 32-bit masks per real.
+ */
+ simd_excl_size = NBNXN_CPU_CLUSTER_I_SIZE*simd_width;
+ snew_aligned(nbat->simd_exclusion_filter1, simd_excl_size, NBNXN_MEM_ALIGN);
+ snew_aligned(nbat->simd_exclusion_filter2, simd_excl_size*2, NBNXN_MEM_ALIGN);
+
+ for (j = 0; j < simd_excl_size; j++)
+ {
+ /* Set the consecutive bits for masking pair exclusions */
+ nbat->simd_exclusion_filter1[j] = (1U << j);
+ nbat->simd_exclusion_filter2[j*2 + 0] = (1U << j);
+ nbat->simd_exclusion_filter2[j*2 + 1] = (1U << j);
+ }
+
+#if (defined GMX_SIMD_IBM_QPX)
+ /* The QPX kernels shouldn't do the bit masking that is done on
+ * x86, because the SIMD units lack bit-wise operations. Instead,
+ * we generate a vector of all 2^4 possible ways an i atom
+ * interacts with its 4 j atoms. Each array entry contains
+ * simd_width signed ints that are read in a single SIMD
+ * load. These ints must contain values that will be interpreted
+ * as true and false when loaded in the SIMD floating-point
+ * registers, ie. any positive or any negative value,
+ * respectively. Each array entry encodes how this i atom will
+ * interact with the 4 j atoms. Matching code exists in
+ * set_ci_top_excls() to generate indices into this array. Those
+ * indices are used in the kernels. */
+
+ simd_excl_size = NBNXN_CPU_CLUSTER_I_SIZE*NBNXN_CPU_CLUSTER_I_SIZE;
+ const int qpx_simd_width = GMX_SIMD_REAL_WIDTH;
+ snew_aligned(simd_interaction_array, simd_excl_size * qpx_simd_width, NBNXN_MEM_ALIGN);
+ for (j = 0; j < simd_excl_size; j++)
+ {
+ int index = j * qpx_simd_width;
+ for (i = 0; i < qpx_simd_width; i++)
+ {
+ simd_interaction_array[index + i] = (j & (1 << i)) ? simdTrue : simdFalse;
+ }
+ }
+ nbat->simd_interaction_array = simd_interaction_array;
+#endif
}
+#endif
/* Initializes an nbnxn_atomdata_t data structure */
void nbnxn_atomdata_init(FILE *fp,
nbnxn_atomdata_t *nbat,
int nb_kernel_type,
- int ntype,const real *nbfp,
+ int enbnxninitcombrule,
+ 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, nth;
+ real c6, c12, tol;
+ char *ptr;
+ gmx_bool simple, bCombGeom, bCombLB, bSIMD;
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 ];
- c12 = nbfp[(i*ntype+i)*2+1];
+ 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)
{
c12 = nbfp[(i*ntype+j)*2+1];
nbat->nbfp[(i*nbat->ntype+j)*2 ] = c6;
nbat->nbfp[(i*nbat->ntype+j)*2+1] = c12;
- c6 /= 6.0;
- c12 /= 12.0;
-
+
+ /* 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;
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 (simple)
+ switch (enbnxninitcombrule)
{
- /* We prefer the geometic combination rule,
- * as that gives a slightly faster kernel than the LB rule.
- */
- if (bCombGeom)
- {
- nbat->comb_rule = ljcrGEOM;
- }
- else if (bCombLB)
- {
- nbat->comb_rule = ljcrLB;
- }
- else
- {
- nbat->comb_rule = ljcrNONE;
-
- nbat->free(nbat->nbfp_comb);
- }
-
- if (fp)
- {
- if (nbat->comb_rule == ljcrNONE)
+ case enbnxninitcombruleDETECT:
+ /* We prefer the geometic combination rule,
+ * as that gives a slightly faster kernel than the LB rule.
+ */
+ if (bCombGeom)
{
- fprintf(fp,"Using full Lennard-Jones parameter combination matrix\n\n");
+ nbat->comb_rule = ljcrGEOM;
+ }
+ else if (bCombLB)
+ {
+ nbat->comb_rule = ljcrLB;
}
else
{
- fprintf(fp,"Using %s Lennard-Jones combination rule\n\n",
- nbat->comb_rule==ljcrGEOM ? "geometric" : "Lorentz-Berthelot");
+ nbat->comb_rule = ljcrNONE;
+
+ nbat->free(nbat->nbfp_comb);
}
- }
- set_combination_rule_data(nbat);
- }
- else
- {
- nbat->comb_rule = ljcrNONE;
+ if (fp)
+ {
+ if (nbat->comb_rule == ljcrNONE)
+ {
+ 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");
+ }
+ }
+ break;
+ case enbnxninitcombruleGEOM:
+ nbat->comb_rule = ljcrGEOM;
+ break;
+ case enbnxninitcombruleLB:
+ nbat->comb_rule = ljcrLB;
+ break;
+ case enbnxninitcombruleNONE:
+ nbat->comb_rule = ljcrNONE;
- nbat->free(nbat->nbfp_comb);
+ nbat->free(nbat->nbfp_comb);
+ break;
+ default:
+ gmx_incons("Unknown enbnxninitcombrule");
}
+ bSIMD = (nb_kernel_type == nbnxnk4xN_SIMD_4xN ||
+ nb_kernel_type == nbnxnk4xN_SIMD_2xNN);
+
+ set_lj_parameter_data(nbat, bSIMD);
+
nbat->natoms = 0;
nbat->type = NULL;
nbat->lj_comb = NULL;
if (simple)
{
- switch (nb_kernel_type)
+ int pack_x;
+
+ if (bSIMD)
+ {
+ 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");
+ }
+ }
+ else
{
- case nbk4xN_X86_SIMD128:
- nbat->XFormat = nbatX4;
- break;
- case nbk4xN_X86_SIMD256:
-#ifndef GMX_DOUBLE
- nbat->XFormat = nbatX8;
-#else
- nbat->XFormat = nbatX4;
-#endif
- 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;
+
+#ifdef GMX_NBNXN_SIMD
+ if (simple)
+ {
+ nbnxn_atomdata_init_simple_exclusion_masks(nbat);
+ }
+#endif
+
+ /* 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;
+ nbat->buffer_flags.flag_nalloc = 0;
+
+ nth = gmx_omp_nthreads_get(emntNonbonded);
+
+ ptr = getenv("GMX_USE_TREEREDUCE");
+ if (ptr != NULL)
+ {
+ nbat->bUseTreeReduce = strtol(ptr, 0, 10);
+ }
+#if defined __MIC__
+ else if (nth > 8) /*on the CPU we currently don't benefit even at 32*/
+ {
+ nbat->bUseTreeReduce = 1;
+ }
+#endif
+ else
+ {
+ nbat->bUseTreeReduce = 0;
+ }
+ if (nbat->bUseTreeReduce)
+ {
+ if (fp)
+ {
+ fprintf(fp, "Using tree force reduction\n\n");
+ }
+ snew(nbat->syncStep, nth);
+ }
}
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,
+/* Sets the atom type in nbnxn_atomdata_t */
+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)
+/* Sets the LJ combination rule parameters in nbnxn_atomdata_t */
+static void nbnxn_atomdata_set_ljcombparams(nbnxn_atomdata_t *nbat,
+ int ngrid,
+ const nbnxn_search_t nbs)
+{
+ int g, i, ncz, ash;
+ const nbnxn_grid_t *grid;
+
+ if (nbat->comb_rule != ljcrNONE)
+ {
+ 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++)
{
+ ncz = grid->cxy_ind[i+1] - grid->cxy_ind[i];
+ ash = (grid->cell0 + grid->cxy_ind[i])*grid->na_sc;
+
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++;
}
}
+/* Set the charges of perturbed atoms in nbnxn_atomdata_t to 0.
+ * This is to automatically remove the RF/PME self term in the nbnxn kernels.
+ * Part of the zero interactions are still calculated in the normal kernels.
+ * All perturbed interactions are calculated in the free energy kernel,
+ * using the original charge and LJ data, not nbnxn_atomdata_t.
+ */
+static void nbnxn_atomdata_mask_fep(nbnxn_atomdata_t *nbat,
+ int ngrid,
+ const nbnxn_search_t nbs)
+{
+ real *q;
+ int stride_q, g, nsubc, c_offset, c, subc, i, ind;
+ const nbnxn_grid_t *grid;
+
+ if (nbat->XFormat == nbatXYZQ)
+ {
+ q = nbat->x + ZZ + 1;
+ stride_q = STRIDE_XYZQ;
+ }
+ else
+ {
+ q = nbat->q;
+ stride_q = 1;
+ }
+
+ for (g = 0; g < ngrid; g++)
+ {
+ grid = &nbs->grid[g];
+ if (grid->bSimple)
+ {
+ nsubc = 1;
+ }
+ else
+ {
+ nsubc = GPU_NSUBCELL;
+ }
+
+ c_offset = grid->cell0*grid->na_sc;
+
+ /* Loop over all columns and copy and fill */
+ for (c = 0; c < grid->nc*nsubc; c++)
+ {
+ /* Does this cluster contain perturbed particles? */
+ if (grid->fep[c] != 0)
+ {
+ for (i = 0; i < grid->na_c; i++)
+ {
+ /* Is this a perturbed particle? */
+ if (grid->fep[c] & (1 << i))
+ {
+ ind = c_offset + c*grid->na_c + i;
+ /* Set atom type and charge to non-interacting */
+ nbat->type[ind] = nbat->ntype - 1;
+ q[ind*stride_q] = 0;
+ }
+ }
+ }
+ }
+ }
+}
+
/* 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++)
+ if (nbat->nenergrp == 1)
+ {
+ return;
+ }
+
+ 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)
+ if (nbs->bFEP)
{
- nbnxn_atomdata_set_energygroups(nbat,ngrid,nbs,atinfo);
+ nbnxn_atomdata_mask_fep(nbat, ngrid, nbs);
}
+
+ /* This must be done after masking types for FEP */
+ nbnxn_atomdata_set_ljcombparams(nbat, ngrid, nbs);
+
+ 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);
+ }
+ }
+ }
+}
+
+static void
+nbnxn_atomdata_clear_reals(real * gmx_restrict dest,
+ int i0, int i1)
+{
+ int i;
+
+ for (i = i0; i < i1; i++)
+ {
+ dest[i] = 0;
+ }
+}
+
+static void
+nbnxn_atomdata_reduce_reals(real * gmx_restrict dest,
+ gmx_bool bDestSet,
+ real ** gmx_restrict src,
+ int nsrc,
+ int i0, int i1)
+{
+ int i, s;
+
+ if (bDestSet)
+ {
+ /* The destination buffer contains data, add to it */
+ for (i = i0; i < i1; i++)
+ {
+ 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++)
+ {
+ dest[i] = src[0][i];
+ for (s = 1; s < nsrc; s++)
+ {
+ dest[i] += src[s][i];
}
}
}
}
+static void
+nbnxn_atomdata_reduce_reals_simd(real gmx_unused * gmx_restrict dest,
+ gmx_bool gmx_unused bDestSet,
+ real gmx_unused ** gmx_restrict src,
+ int gmx_unused nsrc,
+ int gmx_unused i0, int gmx_unused i1)
+{
+#ifdef GMX_NBNXN_SIMD
+/* The SIMD width here is actually independent of that in the kernels,
+ * but we use the same width for simplicity (usually optimal anyhow).
+ */
+ int i, s;
+ gmx_simd_real_t dest_SSE, src_SSE;
+
+ if (bDestSet)
+ {
+ for (i = i0; i < i1; i += GMX_SIMD_REAL_WIDTH)
+ {
+ dest_SSE = gmx_simd_load_r(dest+i);
+ for (s = 0; s < nsrc; s++)
+ {
+ src_SSE = gmx_simd_load_r(src[s]+i);
+ dest_SSE = gmx_simd_add_r(dest_SSE, src_SSE);
+ }
+ gmx_simd_store_r(dest+i, dest_SSE);
+ }
+ }
+ else
+ {
+ for (i = i0; i < i1; i += GMX_SIMD_REAL_WIDTH)
+ {
+ dest_SSE = gmx_simd_load_r(src[0]+i);
+ for (s = 1; s < nsrc; s++)
+ {
+ src_SSE = gmx_simd_load_r(src[s]+i);
+ dest_SSE = gmx_simd_add_r(dest_SSE, src_SSE);
+ }
+ gmx_simd_store_r(dest+i, dest_SSE);
+ }
+ }
+#endif
+}
+
/* Add part of the force array(s) from nbnxn_atomdata_t to f */
static void
nbnxn_atomdata_add_nbat_f_to_f_part(const nbnxn_search_t nbs,
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;
+
+ 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];
+ 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;
+ break;
+ case nbatX4:
+ if (nfa == 1)
+ {
+ fnb = out[0].f;
- for(a=a0; a<a1; a++)
+ 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];
+ }
+ }
+ else
+ {
+ for (a = a0; a < a1; a++)
+ {
+ 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)
{
- i = X4_IND_A(cell[a]);
+ fnb = out[0].f;
- f[a][XX] += fnb[i+XX*PACK_X4];
- f[a][YY] += fnb[i+YY*PACK_X4];
- f[a][ZZ] += fnb[i+ZZ*PACK_X4];
+ 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 = 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 = 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;
- case nbatX8:
- if (nfa == 1)
+ break;
+ default:
+ gmx_incons("Unsupported nbnxn_atomdata_t format");
+ }
+}
+
+static gmx_inline unsigned char reverse_bits(unsigned char b)
+{
+ /* http://graphics.stanford.edu/~seander/bithacks.html#ReverseByteWith64BitsDiv */
+ return (b * 0x0202020202ULL & 0x010884422010ULL) % 1023;
+}
+
+static void nbnxn_atomdata_add_nbat_f_to_f_treereduce(const nbnxn_atomdata_t *nbat,
+ int nth)
+{
+ const nbnxn_buffer_flags_t *flags = &nbat->buffer_flags;
+
+ int next_pow2 = 1<<(gmx_log2i(nth-1)+1);
+
+ assert(nbat->nout == nth); /* tree-reduce currently only works for nout==nth */
+
+ memset(nbat->syncStep, 0, sizeof(*(nbat->syncStep))*nth);
+
+#pragma omp parallel num_threads(nth)
+ {
+ int b0, b1, b;
+ int i0, i1;
+ int group_size, th;
+
+ th = gmx_omp_get_thread_num();
+
+ for (group_size = 2; group_size < 2*next_pow2; group_size *= 2)
{
- fnb = out[0].f;
+ int index[2], group_pos, partner_pos, wu;
+ int partner_th = th ^ (group_size/2);
- for(a=a0; a<a1; a++)
+ if (group_size > 2)
{
- i = X8_IND_A(cell[a]);
+#ifdef TMPI_ATOMICS
+ /* wait on partner thread - replaces full barrier */
+ int sync_th, sync_group_size;
+
+ tMPI_Atomic_memory_barrier(); /* gurantee data is saved before marking work as done */
+ tMPI_Atomic_set(&(nbat->syncStep[th]), group_size/2); /* mark previous step as completed */
+
+ /* find thread to sync with. Equal to partner_th unless nth is not a power of two. */
+ for (sync_th = partner_th, sync_group_size = group_size; sync_th >= nth && sync_group_size > 2; sync_group_size /= 2)
+ {
+ sync_th &= ~(sync_group_size/4);
+ }
+ if (sync_th < nth) /* otherwise nothing to sync index[1] will be >=nout */
+ {
+ /* wait on the thread which computed input data in previous step */
+ while (tMPI_Atomic_get((volatile tMPI_Atomic_t*)&(nbat->syncStep[sync_th])) < group_size/2)
+ {
+ gmx_pause();
+ }
+ /* guarantee that no later load happens before wait loop is finisehd */
+ tMPI_Atomic_memory_barrier();
+ }
+#else /* TMPI_ATOMICS */
+#pragma omp barrier
+#endif
+ }
+
+ /* Calculate buffers to sum (result goes into first buffer) */
+ group_pos = th % group_size;
+ index[0] = th - group_pos;
+ index[1] = index[0] + group_size/2;
- f[a][XX] += fnb[i+XX*PACK_X8];
- f[a][YY] += fnb[i+YY*PACK_X8];
- f[a][ZZ] += fnb[i+ZZ*PACK_X8];
+ /* If no second buffer, nothing to do */
+ if (index[1] >= nbat->nout && group_size > 2)
+ {
+ continue;
+ }
+
+#if NBNXN_BUFFERFLAG_MAX_THREADS > 256
+#error reverse_bits assumes max 256 threads
+#endif
+ /* Position is permuted so that one of the 2 vectors being added was computed on the same thread in the previous step.
+ This improves locality and enables to sync with just a single thread between steps (=the levels in the btree).
+ The permutation which allows this corresponds to reversing the bits of the group position.
+ */
+ group_pos = reverse_bits(group_pos)/(256/group_size);
+
+ partner_pos = group_pos ^ 1;
+
+ /* loop over two work-units (own and partner) */
+ for (wu = 0; wu < 2; wu++)
+ {
+ if (wu == 1)
+ {
+ if (partner_th < nth)
+ {
+ break; /* partner exists we don't have to do his work */
+ }
+ else
+ {
+ group_pos = partner_pos;
+ }
+ }
+
+ /* Calculate the cell-block range for our thread */
+ b0 = (flags->nflag* group_pos )/group_size;
+ b1 = (flags->nflag*(group_pos+1))/group_size;
+
+ for (b = b0; b < b1; b++)
+ {
+ i0 = b *NBNXN_BUFFERFLAG_SIZE*nbat->fstride;
+ i1 = (b+1)*NBNXN_BUFFERFLAG_SIZE*nbat->fstride;
+
+ if ((flags->flag[b] & (1ULL<<index[1])) || group_size > 2)
+ {
+#ifdef GMX_NBNXN_SIMD
+ nbnxn_atomdata_reduce_reals_simd
+#else
+ nbnxn_atomdata_reduce_reals
+#endif
+ (nbat->out[index[0]].f,
+ (flags->flag[b] & (1ULL<<index[0])) || group_size > 2,
+ &(nbat->out[index[1]].f), 1, i0, i1);
+
+ }
+ else if (!(flags->flag[b] & (1ULL<<index[0])))
+ {
+ nbnxn_atomdata_clear_reals(nbat->out[index[0]].f,
+ i0, i1);
+ }
+ }
}
}
- else
+ }
+}
+
+
+static void nbnxn_atomdata_add_nbat_f_to_f_stdreduce(const nbnxn_atomdata_t *nbat,
+ int nth)
+{
+ int th;
+#pragma omp parallel for num_threads(nth) schedule(static)
+ for (th = 0; th < nth; th++)
+ {
+ const nbnxn_buffer_flags_t *flags;
+ int b0, b1, b;
+ int i0, i1;
+ int nfptr;
+ real *fptr[NBNXN_BUFFERFLAG_MAX_THREADS];
+ int out;
+
+ flags = &nbat->buffer_flags;
+
+ /* Calculate the cell-block range for our thread */
+ b0 = (flags->nflag* th )/nth;
+ b1 = (flags->nflag*(th+1))/nth;
+
+ for (b = b0; b < b1; b++)
{
- for(a=a0; a<a1; a++)
+ i0 = b *NBNXN_BUFFERFLAG_SIZE*nbat->fstride;
+ i1 = (b+1)*NBNXN_BUFFERFLAG_SIZE*nbat->fstride;
+
+ nfptr = 0;
+ for (out = 1; out < nbat->nout; out++)
{
- i = X8_IND_A(cell[a]);
-
- for(fa=0; fa<nfa; fa++)
+ if (flags->flag[b] & (1U<<out))
{
- 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];
+ fptr[nfptr++] = nbat->out[out].f;
}
}
+ if (nfptr > 0)
+ {
+#ifdef GMX_NBNXN_SIMD
+ nbnxn_atomdata_reduce_reals_simd
+#else
+ nbnxn_atomdata_reduce_reals
+#endif
+ (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);
+ }
}
- 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);
+
+ if (nbat->nout > 1)
+ {
+ if (locality != eatAll)
+ {
+ gmx_incons("add_f_to_f called with nout>1 and locality!=eatAll");
+ }
+
+ /* Reduce the force thread output buffers into buffer 0, before adding
+ * them to the, differently ordered, "real" force buffer.
+ */
+ if (nbat->bUseTreeReduce)
+ {
+ nbnxn_atomdata_add_nbat_f_to_f_treereduce(nbat, nth);
+ }
+ else
+ {
+ nbnxn_atomdata_add_nbat_f_to_f_stdreduce(nbat, nth);
+ }
+ }
#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,
- nbat->out,
- nbat->nout,
- a0+((th+0)*na)/nth,
- a0+((th+1)*na)/nth,
- f);
+ nbnxn_atomdata_add_nbat_f_to_f_part(nbs, nbat,
+ nbat->out,
+ 1,
+ a0+((th+0)*na)/nth,
+ a0+((th+1)*na)/nth,
+ f);
}
nbs_cycle_stop(&nbs->cc[enbsCCreducef]);
/* 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