/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2005,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2005,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016,2017, 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.
{
int atnr;
- if (dd == NULL)
+ if (dd == nullptr)
{
atnr = i + 1;
}
static void vec_rvec_init(vec_rvec_t *v)
{
v->nalloc = 0;
- v->v = NULL;
+ v->v = nullptr;
}
static void vec_rvec_check_alloc(vec_rvec_t *v, int n)
consider PBC in the treatment of fshift */
bShiftForcesNeedPbc = (dd->ci[dd->dim[d]] == 0);
bScrew = (bShiftForcesNeedPbc && dd->bScrewPBC && dd->dim[d] == XX);
- if (fshift == NULL && !bScrew)
+ if (fshift == nullptr && !bScrew)
{
bShiftForcesNeedPbc = FALSE;
}
static void dd_collect_cg(gmx_domdec_t *dd,
t_state *state_local)
{
- gmx_domdec_master_t *ma = NULL;
- int buf2[2], *ibuf, i, ncg_home = 0, *cg = NULL, nat_home = 0;
+ gmx_domdec_master_t *ma = nullptr;
+ int buf2[2], *ibuf, i, ncg_home = 0, *cg = nullptr, nat_home = 0;
if (state_local->ddp_count == dd->comm->master_cg_ddp_count)
{
}
else
{
- ibuf = NULL;
+ ibuf = nullptr;
}
/* Collect the charge group and atom counts on the master */
dd_gather(dd, 2*sizeof(int), buf2, ibuf);
/* Collect the charge group indices on the master */
dd_gatherv(dd,
ncg_home*sizeof(int), cg,
- DDMASTER(dd) ? ma->ibuf : NULL,
- DDMASTER(dd) ? ma->ibuf+dd->nnodes : NULL,
- DDMASTER(dd) ? ma->cg : NULL);
+ DDMASTER(dd) ? ma->ibuf : nullptr,
+ DDMASTER(dd) ? ma->ibuf+dd->nnodes : nullptr,
+ DDMASTER(dd) ? ma->cg : nullptr);
dd->comm->master_cg_ddp_count = state_local->ddp_count;
}
{
gmx_domdec_master_t *ma;
int n, i, c, a, nalloc = 0;
- rvec *buf = NULL;
+ rvec *buf = nullptr;
t_block *cgs_gl;
ma = dd->ma;
const rvec *lv, rvec *v)
{
gmx_domdec_master_t *ma;
- int *rcounts = NULL, *disps = NULL;
+ int *rcounts = nullptr, *disps = nullptr;
int n, i, c, a;
- rvec *buf = NULL;
+ rvec *buf = nullptr;
t_block *cgs_gl;
ma = dd->ma;
}
}
- if (f != NULL)
+ if (f != nullptr)
{
(*f).resize(natoms + 1);
}
{
gmx_domdec_master_t *ma;
int n, i, c, a, nalloc = 0;
- rvec *buf = NULL;
+ rvec *buf = nullptr;
if (DDMASTER(dd))
{
rvec *v, rvec *lv)
{
gmx_domdec_master_t *ma;
- int *scounts = NULL, *disps = NULL;
+ int *scounts = nullptr, *disps = nullptr;
int n, i, c, a;
- rvec *buf = NULL;
+ rvec *buf = nullptr;
if (DDMASTER(dd))
{
static void dd_distribute_dfhist(gmx_domdec_t *dd, df_history_t *dfhist)
{
- if (dfhist == NULL)
+ if (dfhist == nullptr)
{
return;
}
copy_mat(state->boxv, state_local->boxv);
copy_mat(state->svir_prev, state_local->svir_prev);
copy_mat(state->fvir_prev, state_local->fvir_prev);
- if (state->dfhist != NULL)
+ if (state->dfhist != nullptr)
{
copy_df_history(state_local->dfhist, state->dfhist);
}
static void write_dd_grid_pdb(const char *fn, gmx_int64_t step,
gmx_domdec_t *dd, matrix box, gmx_ddbox_t *ddbox)
{
- rvec grid_s[2], *grid_r = NULL, cx, r;
+ rvec grid_s[2], *grid_r = nullptr, cx, r;
char fname[STRLEN], buf[22];
FILE *out;
int a, i, d, z, y, x;
snew(grid_r, 2*dd->nnodes);
}
- dd_gather(dd, 2*sizeof(rvec), grid_s, DDMASTER(dd) ? grid_r : NULL);
+ dd_gather(dd, 2*sizeof(rvec), grid_s, DDMASTER(dd) ? grid_r : nullptr);
if (DDMASTER(dd))
{
/* This assumes DD cells with identical x coordinates
* are numbered sequentially.
*/
- if (dd->comm->pmenodes == NULL)
+ if (dd->comm->pmenodes == nullptr)
{
if (sim_nodeid < dd->nnodes)
{
void get_pme_nnodes(const gmx_domdec_t *dd,
int *npmenodes_x, int *npmenodes_y)
{
- if (dd != NULL)
+ if (dd != nullptr)
{
*npmenodes_x = dd->comm->npmenodes_x;
*npmenodes_y = dd->comm->npmenodes_y;
int *cginfo;
int cg;
- if (fr != NULL)
+ if (fr != nullptr)
{
cginfo_mb = fr->cginfo_mb;
cginfo = fr->cginfo;
}
}
- if (bLocalCG != NULL)
+ if (bLocalCG != nullptr)
{
for (cg = cg0; cg < cg1; cg++)
{
int i, ngl, nerr;
nerr = 0;
- if (bLocalCG == NULL)
+ if (bLocalCG == nullptr)
{
return nerr;
}
{
cellsize_min[d] = ddbox->box_size[d]*ddbox->skew_fac[d];
npulse[d] = 1;
- if (dd->nc[d] == 1 || comm->slb_frac[d] == NULL)
+ if (dd->nc[d] == 1 || comm->slb_frac[d] == nullptr)
{
/* Uniform grid */
cell_dx = ddbox->box_size[d]/dd->nc[d];
for (d = 0; d < comm->npmedecompdim; d++)
{
set_pme_maxshift(dd, &comm->ddpme[d],
- comm->slb_frac[dd->dim[d]] == NULL, ddbox,
+ comm->slb_frac[dd->dim[d]] == nullptr, ddbox,
comm->ddpme[d].slb_dim_f);
}
}
srenew(cd->ind, np);
for (i = cd->np_nalloc; i < np; i++)
{
- cd->ind[i].index = NULL;
+ cd->ind[i].index = nullptr;
cd->ind[i].nalloc = 0;
}
cd->np_nalloc = np;
gmx_domdec_t *dd)
{
gmx_domdec_master_t *ma;
- int **tmp_ind = NULL, *tmp_nalloc = NULL;
+ int **tmp_ind = nullptr, *tmp_nalloc = nullptr;
int i, icg, j, k, k0, k1, d;
matrix tcm;
rvec cg_cm;
t_block *cgs, matrix box, gmx_ddbox_t *ddbox,
rvec pos[])
{
- gmx_domdec_master_t *ma = NULL;
+ gmx_domdec_master_t *ma = nullptr;
ivec npulse;
int i, cg_gl;
int *ibuf, buf2[2] = { 0, 0 };
}
else
{
- ibuf = NULL;
+ ibuf = nullptr;
}
dd_scatter(dd, 2*sizeof(int), ibuf, buf2);
}
dd_scatterv(dd,
- bMaster ? ma->ibuf : NULL,
- bMaster ? ma->ibuf+dd->nnodes : NULL,
- bMaster ? ma->cg : NULL,
+ bMaster ? ma->ibuf : nullptr,
+ bMaster ? ma->ibuf+dd->nnodes : nullptr,
+ bMaster ? ma->cg : nullptr,
dd->ncg_home*sizeof(int), dd->index_gl);
/* Determine the home charge group sizes */
gmx_bool bV = FALSE, bCGP = FALSE;
real pos_d;
matrix tcm;
- rvec *cg_cm = NULL, cell_x0, cell_x1, limitd, limit0, limit1;
+ rvec *cg_cm = nullptr, cell_x0, cell_x1, limitd, limit0, limit1;
int *cgindex;
cginfo_mb_t *cginfo_mb;
gmx_domdec_comm_t *comm;
* for the normal loops and again half it for water loops.
*/
name = nrnb_str(i);
- if (strstr(name, "W3") != NULL || strstr(name, "W4") != NULL)
+ if (strstr(name, "W3") != nullptr || strstr(name, "W4") != nullptr)
{
sum += nrnb->n[i]*0.25*cost_nrnb(i);
}
for (i = eNR_NBKERNEL_FREE_ENERGY; i <= eNR_NB14; i++)
{
name = nrnb_str(i);
- if (strstr(name, "W3") != NULL || strstr(name, "W4") != NULL)
+ if (strstr(name, "W3") != nullptr || strstr(name, "W4") != nullptr)
{
sum += nrnb->n[i]*cost_nrnb(i);
}
{
gmx_domdec_comm_t *comm;
domdec_load_t *load;
- domdec_root_t *root = NULL;
+ domdec_root_t *root = nullptr;
int d, dim, i, pos;
float cell_frac = 0, sbuf[DD_NLOAD_MAX];
gmx_bool bSepPME;
if (dd->nnodes <= GMX_DD_NNODES_SENDRECV)
{
- ma->vbuf = NULL;
+ ma->vbuf = nullptr;
}
else
{
* Real reordering is only supported on very few architectures,
* Blue Gene is one of them.
*/
- CartReorder = (getenv("GMX_NO_CART_REORDER") == NULL);
+ CartReorder = (getenv("GMX_NO_CART_REORDER") == nullptr);
if (cr->npmenodes > 0)
{
int i, n;
double dbl;
- slb_frac = NULL;
- if (nc > 1 && size_string != NULL)
+ slb_frac = nullptr;
+ if (nc > 1 && size_string != nullptr)
{
if (fplog)
{
int dim;
dd->ndim = 0;
- if (getenv("GMX_DD_ORDER_ZYX") != NULL)
+ if (getenv("GMX_DD_ORDER_ZYX") != nullptr)
{
/* Decomposition order z,y,x */
if (fplog)
}
comm->nalloc_int = 0;
- comm->buf_int = NULL;
+ comm->buf_int = nullptr;
vec_rvec_init(&comm->vbuf);
dd->bScrewPBC = (ir->ePBC == epbcSCREW);
dd->pme_recv_f_alloc = 0;
- dd->pme_recv_f_buf = NULL;
+ dd->pme_recv_f_buf = nullptr;
/* Initialize to GPU share count to 0, might change later */
comm->nrank_gpu_shared = 0;
}
else
{
- set_ddbox_cr(cr, NULL, ir, box, &comm->cgs_gl, x, ddbox);
+ set_ddbox_cr(cr, nullptr, ir, box, &comm->cgs_gl, x, ddbox);
/* We need to choose the optimal DD grid and possibly PME nodes */
real limit =
*/
if (dd->ndim >= 2 && dd->dim[0] == XX && dd->dim[1] == YY &&
comm->npmenodes > dd->nc[XX] && comm->npmenodes % dd->nc[XX] == 0 &&
- getenv("GMX_PMEONEDD") == NULL)
+ getenv("GMX_PMEONEDD") == nullptr)
{
comm->npmedecompdim = 2;
comm->npmenodes_x = dd->nc[XX];
else
{
/* Only communicate atoms based on cut-off */
- comm->cglink = NULL;
- comm->bLocalCG = NULL;
+ comm->cglink = nullptr;
+ comm->bLocalCG = nullptr;
}
}
real limit, shrink;
char buf[64];
- if (fplog == NULL)
+ if (fplog == nullptr)
{
return;
}
real r_comm2, r_bcomm2;
dd_corners_t corners;
ivec tric_dist;
- rvec *cg_cm, *normal, *v_d, *v_0 = NULL, *v_1 = NULL, *recv_vr;
+ rvec *cg_cm, *normal, *v_d, *v_0 = nullptr, *v_1 = nullptr, *recv_vr;
real skew_fac2_d, skew_fac_01;
rvec sf2_round;
int nsend, nat;
break;
default:
gmx_incons("unimplemented");
- cg_cm = NULL;
+ cg_cm = nullptr;
}
for (dim_ind = 0; dim_ind < dd->ndim; dim_ind++)
* So we pass NULL for the forcerec.
*/
dd_set_cginfo(dd->index_gl, dd->ncg_home, dd->ncg_tot,
- NULL, comm->bLocalCG);
+ nullptr, comm->bLocalCG);
}
if (debug)
{
int a, atot, cg, cg0, cg1, i;
- if (cgindex == NULL)
+ if (cgindex == nullptr)
{
/* Avoid the useless loop of the atoms within a cg */
order_vec_cg(ncg, sort, v, buf);
}
else
{
- cgindex = NULL;
+ cgindex = nullptr;
}
/* Remove the charge groups which are no longer at home here */
gmx_sumd(ddnatNR-ddnatZONE, comm->sum_nat, cr);
- if (fplog == NULL)
+ if (fplog == nullptr)
{
return;
}
comm->zones.dens_zone0,
fr->cginfo,
as_rvec_array(state_local->x.data()),
- ncg_moved, bRedist ? comm->moved : NULL,
+ ncg_moved, bRedist ? comm->moved : nullptr,
fr->nbv->grp[eintLocal].kernel_type,
fr->nbv->grp[eintLocal].nbat);
/* Update atom data for mdatoms and several algorithms */
mdAlgorithmsSetupAtomData(cr, ir, top_global, top_local, fr,
- NULL, mdatoms, vsite, NULL);
+ nullptr, mdatoms, vsite, nullptr);
if (ir->implicit_solvent)
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff