void p_graph(FILE *log, const char *title, t_graph *g)
{
int i, j;
const char *cc[egcolNR] = { "W", "G", "B" };
GCHECK(g);
fprintf(log, "graph: %s\n", title);
fprintf(log, "nnodes: %d\n", g->nnodes);
fprintf(log, "nbound: %d\n", g->nbound);
fprintf(log, "start: %d\n", g->at_start);
fprintf(log, "end: %d\n", g->at_end);
fprintf(log, " atom shiftx shifty shiftz C nedg e1 e2 etc.\n");
for (i = 0; (i < g->nnodes); i++)
{
if (g->nedge[i] > 0)
{
fprintf(log, "%5d%7d%7d%7d %1s%5d", g->at_start+i+1,
g->ishift[g->at_start+i][XX],
g->ishift[g->at_start+i][YY],
g->ishift[g->at_start+i][ZZ],
(g->negc > 0) ? cc[g->egc[i]] : " ",
g->nedge[i]);
for (j = 0; (j < g->nedge[i]); j++)
{
fprintf(log, " %5d", g->edge[i][j]+1);
}
fprintf(log, "\n");
}
}
fflush(log);
}
void done_graph(t_graph *g)
{
GCHECK(g);
if (g->nnodes > 0)
{
sfree(g->nedge);
sfree(g->edge[0]);
sfree(g->edge);
sfree(g->egc);
}
sfree(g->ishift);
}
void testGetFundamental(TestScriptContext * context)
{
QVAR(f = 100)
QVAR(s = "abc")
GVariant v;
if(context->getBindingLib()) {
v = scriptGetValue(context->getBindingLib(), "f").toFundamental();
GCHECK(fromVariant<int>(v) == 100);
v = scriptGetValue(context->getBindingLib(), "s").toFundamental();
GCHECK(v.isEmpty());
}
if(context->getBindingApi()) {
v = scriptGetValue(context->getBindingApi(), "f").toFundamental();
GCHECK(fromVariant<int>(v) == 100);
v = scriptGetValue(context->getBindingApi(), "s").toFundamental();
GCHECK(v.isEmpty());
}
}
void shift_x(const t_graph *g, matrix box, const rvec x[], rvec x_s[])
{
ivec *is;
int g0, g1;
int j, tx, ty, tz;
GCHECK(g);
g0 = g->at_start;
g1 = g->at_end;
is = g->ishift;
for (j = g->at0; j < g0; j++)
{
copy_rvec(x[j], x_s[j]);
}
if (g->bScrewPBC)
{
for (j = g0; (j < g1); j++)
{
tx = is[j][XX];
ty = is[j][YY];
tz = is[j][ZZ];
if ((tx > 0 && tx % 2 == 1) ||
(tx < 0 && -tx %2 == 1))
{
x_s[j][XX] = x[j][XX] + tx*box[XX][XX];
x_s[j][YY] = box[YY][YY] + box[ZZ][YY] - x[j][YY];
x_s[j][ZZ] = box[ZZ][ZZ] - x[j][ZZ];
}
else
{
x_s[j][XX] = x[j][XX];
}
x_s[j][YY] = x[j][YY] + ty*box[YY][YY] + tz*box[ZZ][YY];
x_s[j][ZZ] = x[j][ZZ] + tz*box[ZZ][ZZ];
}
}
else if (TRICLINIC(box))
{
for (j = g0; (j < g1); j++)
{
tx = is[j][XX];
ty = is[j][YY];
tz = is[j][ZZ];
x_s[j][XX] = x[j][XX]+tx*box[XX][XX]+ty*box[YY][XX]+tz*box[ZZ][XX];
x_s[j][YY] = x[j][YY]+ty*box[YY][YY]+tz*box[ZZ][YY];
x_s[j][ZZ] = x[j][ZZ]+tz*box[ZZ][ZZ];
}
}
else
{
for (j = g0; (j < g1); j++)
{
tx = is[j][XX];
ty = is[j][YY];
tz = is[j][ZZ];
x_s[j][XX] = x[j][XX]+tx*box[XX][XX];
x_s[j][YY] = x[j][YY]+ty*box[YY][YY];
x_s[j][ZZ] = x[j][ZZ]+tz*box[ZZ][ZZ];
}
}
for (j = g1; j < g->at1; j++)
{
copy_rvec(x[j], x_s[j]);
}
}
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");
}
}
}
}
