/* Important function. */
void
mtype_zfree (const char *file, int line, int type, void *ptr)
{
mstat[type].t_free++;
mtype_log ("xfree", ptr, file, line, type);
ze_free (type, ptr);
}
/* run simulation */
int run(void)
{
gmx_mtop_t *mtop;
int i, ndata, nat, rescnt = 0;
char fxtc[FILENAME_MAX] = "";
char *ftop;
matrix box;
rvec *xref = NULL, *xrefbb = NULL;
zedata_t *ze = NULL;
trj_t *trj = NULL;
double dt, bref = 1.0/(BOLTZ*Tref), wtot = 0.0;
hist_t *hsrms = NULL;
bb_t *bb = NULL;
FILE *fplog = NULL;
memset(box, 0, sizeof(box));
/* read topology and the reference structure */
die_if ((ftop = nfexists(fntop, 7)) == NULL, "no topology file %s\n", fntop);
mtop = read_tpx_conf(ftop, &xref, box, &nat, &dt);
printf("using the structure in %s as the reference\n", ftop);
bb = init_index(&rescnt, mtop); /* get indices for backbone dihedrals */
xnew(xrefbb, rescnt * 3);
xgetbb(xrefbb, xref, bb, rescnt);
hsrms = hs_open(1, 0.0, xmax, xdel);
if (fnlog) {
xfopen(fplog, fnlog, "w", exit(1));
}
if (fndist2 != NULL) {
/* if there's a second database, combine it with the first database */
die_if (0 != hs_load(hsrms, fndist, HIST_VERBOSE),
"cannot load master %s\n", fndist);
die_if (0 != hs_load(hsrms, fndist2, HIST_VERBOSE|HIST_ADDITION),
"cannot add the second %s\n", fndist2);
} else {
/* if there's no second database, we accumulate trajectories */
/* 1. initialize multiple histogram weights for tempering */
if (!ctmd) {
if ((ze = ze_load(fnze, 10)) == NULL) {
fprintf(stderr, "cannot load %s\n", fnze);
return -1;
}
/* we first load TRACE, compute weight of each frame */
if ((trj = trj_loadseq(fntr, &ndata, dt, tequil,
ze, bref, delbet)) == NULL) {
fprintf(stderr, "failed to load trace\n");
return -1;
}
} else {
/* for regular MD, set ndata to a large number */
ndata = 10000000;
}
/* 2. we now successively load xtc from each data dir,
* try to match the TRACE frames */
if (!ctmd) trj->pos = 0;
for (i = 1; i <= ndata; i++) {
sprintf(fxtc, "data%d/%s", i, fnxtc);
if (!fexists(fxtc)) { /* test if the file exists */
die_if(!ctmd, "cannot read %s\n", fnxtc);
break;
}
if (0 != dotrj(hsrms, bb, rescnt, fplog,
trj, fxtc, xrefbb, nat, box, &wtot)) {
fprintf(stderr, "error doing %s\n", fnxtc);
return -1;
}
}
}
hs_save(hsrms, fndist, HIST_ADDAHALF|HIST_VERBOSE);
hs_close(hsrms);
sfree(mtop);
if (!ctmd) {
if (trj) trj_free(trj);
if (ze) ze_free(ze);
}
free(xrefbb);
return 0;
}