static void write_constr_pdb(const char *fn, const char *title,
gmx_mtop_t *mtop,
int start, int homenr, t_commrec *cr,
rvec x[], matrix box)
{
char fname[STRLEN], format[STRLEN];
FILE *out;
int dd_ac0 = 0, dd_ac1 = 0, i, ii, resnr;
gmx_domdec_t *dd;
char *anm, *resnm;
dd = NULL;
if (DOMAINDECOMP(cr))
{
dd = cr->dd;
dd_get_constraint_range(dd, &dd_ac0, &dd_ac1);
start = 0;
homenr = dd_ac1;
}
if (PAR(cr))
{
sprintf(fname, "%s_n%d.pdb", fn, cr->sim_nodeid);
}
else
{
sprintf(fname, "%s.pdb", fn);
}
sprintf(format, "%s\n", get_pdbformat());
out = gmx_fio_fopen(fname, "w");
fprintf(out, "TITLE %s\n", title);
gmx_write_pdb_box(out, -1, box);
for (i = start; i < start+homenr; i++)
{
if (dd != NULL)
{
if (i >= dd->nat_home && i < dd_ac0)
{
continue;
}
ii = dd->gatindex[i];
}
else
{
ii = i;
}
gmx_mtop_atominfo_global(mtop, ii, &anm, &resnr, &resnm);
fprintf(out, format, "ATOM", (ii+1)%100000,
anm, resnm, ' ', resnr%10000, ' ',
10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ]);
}
fprintf(out, "TER\n");
gmx_fio_fclose(out);
}
int init_mmcg( int nfile, // number of files
const t_filenm fnm[], // file names
t_inputrec* ir, // input record and box stuff
gmx_mtop_t *top_global, // global topology
int *allcgnr, // charge groups number
int *allcgid[], // charge groups ids
int *allsolnr, // solvent groups number
int *allsolid[], // solvent groups ids
t_commrec *cr // communicators
)
{
char *mmcgf, *topf, line[STRLEN+1], strtmp[STRLEN+1], *pos;
FILE *mmcgfp, *topfp;
int k0,k=0,i,resnr;
int icg,cg0,cg1;
int allatresnr, *allatresid;
t_block all_cgs;
all_cgs = gmx_mtop_global_cgs(top_global); // index of cgs for whole system
mmcgf = ftp2fn(efGMX,nfile,fnm);
if((mmcgfp = fopen(mmcgf,"r"))==NULL)
{ // opening-of mmcg-data failed
fprintf(stderr, "ERROR : Impossible to open the mmcg-data file\n");
return 1;
}
while (!feof(mmcgfp))
{ // counting lines in mmcg-data file
if (fgets (line,STRLEN+1,mmcgfp)) allatresnr++;
}
// reading mmcg data
snew (allatresid,allatresnr);
rewind (mmcgfp);
for (i=0,k=0; i<allatresnr;i++) {
fgets(line,STRLEN+1,mmcgfp);
if(line[0] == '#') {
if(strstr(line,"nstwtlist")) { // number of step for list regeneration
pos = strchr(line,'='); pos++;
ir->mmcg.nstwtlist = atoi(pos);
}
else if (strstr(line,"shell1wt")) { // inner limit of water droplet
pos = strchr(line,'='); pos++;
ir->mmcg.shell1wt = atoi(pos);
}
else if (strstr(line,"shell2wt")) { // outer limit of water droplet
pos = strchr(line,'='); pos++;
ir->mmcg.shell2wt = atoi(pos);
}
continue;
}
// reading all-atoms resids
allatresid[k] = atoi(line);
if(allatresid[k] != 0) k++;
} // end for, mmcg file scanning
allatresnr = k;
if (cr->nnodes!=1) gmx_barrier(cr);
fclose(mmcgfp);
// printing all-atoms resids in the log file
fprintf(log,"MM/CG : gmx_resids: %d\n", allatresnr);
for(i=0; i<allatresnr;i++)
fprintf (log, " %d\n", allatresid[i]);
fprintf(log,"\n");
// internal enumeration
for (i=0; i<allatresnr;i++) (allatresid[i])--;
// allocating charge groups and solvent
snew(*allcgid, ncg_mtop(top_global));
int maxsol;
// It seems that GROMACS did not store the correct number of solvent
// molecules in top_global... At this point the value of nmol is more than 10 million!
// => srenew() at the end of the routine when allsolnr will be computed
int moltype_id=0;
while (strcmp(top_global->moltype->name[moltype_id],"SOL")) {
moltype_id++;
}
maxsol = top_global->molblock[moltype_id].nmol;
MPI_Bcast(&maxsol,1,MPI_INT,0,cr->mpi_comm_mysim);
snew(*allsolid, maxsol);
// charge groups to monitor, first and last indices
cg0 = 0;
cg1 = ncg_mtop(top_global);
char **atomname_=NULL,**resname_=NULL; // we need these to get the information of atoms
// cf. mtop_utils.h
for(icg=cg0; icg<cg1; icg++) {
// get residue number and name of the cg's first atom
k0 = all_cgs.index[icg];
gmx_mtop_atominfo_global(top_global,k0,&atomname_,&resnr,&resname_);
if (!strcmp(resname_,"SOL")) { // Water
(*allsolid)[*allsolnr] = icg;
(*allsolnr)++; // counting waters
}
for (i=0; i<allatresnr; i++) {
if (resnr == allatresid[i]) { // touché !
(*allcgid)[*allcgnr] = icg;
(*allcgnr)++; // counting cg
}
}
}
if(cr->nnodes!=1) gmx_barrier(cr);
return 0;
}
