void mk_mshift(FILE *log, t_graph *g, int ePBC,
matrix box, const rvec x[])
{
static int nerror_tot = 0;
int npbcdim;
int ng, nnodes, i;
int nW, nG, nB; /* Number of Grey, Black, White */
int fW, fG; /* First of each category */
int nerror = 0;
g->bScrewPBC = (ePBC == epbcSCREW);
if (ePBC == epbcXY)
{
npbcdim = 2;
}
else
{
npbcdim = 3;
}
GCHECK(g);
/* This puts everything in the central box, that is does not move it
* at all. If we return without doing this for a system without bonds
* (i.e. only settles) all water molecules are moved to the opposite octant
*/
for (i = g->at0; (i < g->at1); i++)
{
g->ishift[i][XX] = g->ishift[i][YY] = g->ishift[i][ZZ] = 0;
}
if (!g->nbound)
{
return;
}
nnodes = g->nnodes;
if (nnodes > g->negc)
{
g->negc = nnodes;
srenew(g->egc, g->negc);
}
memset(g->egc, 0, (size_t)(nnodes*sizeof(g->egc[0])));
nW = g->nbound;
nG = 0;
nB = 0;
fW = 0;
/* We even have a loop invariant:
* nW+nG+nB == g->nbound
*/
#ifdef DEBUG2
fprintf(log, "Starting W loop\n");
#endif
while (nW > 0)
{
/* Find the first white, this will allways be a larger
* number than before, because no nodes are made white
* in the loop
*/
if ((fW = first_colour(fW, egcolWhite, g, g->egc)) == -1)
{
gmx_fatal(FARGS, "No WHITE nodes found while nW=%d\n", nW);
}
/* Make the first white node grey */
g->egc[fW] = egcolGrey;
nG++;
nW--;
/* Initial value for the first grey */
fG = fW;
#ifdef DEBUG2
fprintf(log, "Starting G loop (nW=%d, nG=%d, nB=%d, total %d)\n",
nW, nG, nB, nW+nG+nB);
#endif
while (nG > 0)
{
if ((fG = first_colour(fG, egcolGrey, g, g->egc)) == -1)
{
gmx_fatal(FARGS, "No GREY nodes found while nG=%d\n", nG);
}
/* Make the first grey node black */
g->egc[fG] = egcolBlack;
nB++;
nG--;
/* Make all the neighbours of this black node grey
* and set their periodicity
*/
ng = mk_grey(g->egc, g, &fG, npbcdim, box, x, &nerror);
/* ng is the number of white nodes made grey */
nG += ng;
nW -= ng;
}
}
if (nerror > 0)
{
nerror_tot++;
if (nerror_tot <= 100)
{
fprintf(stderr, "There were %d inconsistent shifts. Check your topology\n",
nerror);
if (log)
{
fprintf(log, "There were %d inconsistent shifts. Check your topology\n",
nerror);
}
}
if (nerror_tot == 100)
{
fprintf(stderr, "Will stop reporting inconsistent shifts\n");
if (log)
{
fprintf(log, "Will stop reporting inconsistent shifts\n");
}
}
}
}
static int mk_sblocks(FILE *fp, t_graph *g, int maxsid, t_sid sid[])
{
int ng, nnodes;
int nW, nG, nB; /* Number of Grey, Black, White */
int fW, fG; /* First of each category */
egCol *egc = NULL; /* The colour of each node */
int g0, nblock;
if (!g->nbound)
{
return 0;
}
nblock = 0;
nnodes = g->nnodes;
snew(egc, nnodes);
g0 = g->at_start;
nW = g->nbound;
nG = 0;
nB = 0;
fW = 0;
/* We even have a loop invariant:
* nW+nG+nB == g->nbound
*/
if (fp)
{
fprintf(fp, "Walking down the molecule graph to make constraint-blocks\n");
}
while (nW > 0)
{
/* Find the first white, this will allways be a larger
* number than before, because no nodes are made white
* in the loop
*/
if ((fW = first_colour(fW, egcolWhite, g, egc)) == -1)
{
gmx_fatal(FARGS, "No WHITE nodes found while nW=%d\n", nW);
}
/* Make the first white node grey, and set the block number */
egc[fW] = egcolGrey;
range_check(fW+g0, 0, maxsid);
sid[fW+g0].sid = nblock++;
nG++;
nW--;
/* Initial value for the first grey */
fG = fW;
if (debug)
{
fprintf(debug, "Starting G loop (nW=%d, nG=%d, nB=%d, total %d)\n",
nW, nG, nB, nW+nG+nB);
}
while (nG > 0)
{
if ((fG = first_colour(fG, egcolGrey, g, egc)) == -1)
{
gmx_fatal(FARGS, "No GREY nodes found while nG=%d\n", nG);
}
/* Make the first grey node black */
egc[fG] = egcolBlack;
nB++;
nG--;
/* Make all the neighbours of this black node grey
* and set their block number
*/
ng = mk_grey(egc, g, &fG, maxsid, sid);
/* ng is the number of white nodes made grey */
nG += ng;
nW -= ng;
}
}
sfree(egc);
if (debug)
{
fprintf(debug, "Found %d shake blocks\n", nblock);
}
return nblock;
}
