static void par_fn(char *base, int ftp, const t_commrec *cr,
gmx_bool bAppendSimId, gmx_bool bAppendNodeId,
char buf[], int bufsize)
{
if ((size_t)bufsize < (strlen(base)+10))
{
gmx_mem("Character buffer too small!");
}
/* Copy to buf, and strip extension */
strcpy(buf, base);
buf[strlen(base) - strlen(ftp2ext(fn2ftp(base))) - 1] = '\0';
if (bAppendSimId)
{
sprintf(buf+strlen(buf), "%d", cr->ms->sim);
}
if (bAppendNodeId)
{
strcat(buf, "_rank");
sprintf(buf+strlen(buf), "%d", cr->nodeid);
}
strcat(buf, ".");
/* Add extension again */
strcat(buf, (ftp == efTPX) ? "tpr" : (ftp == efEDR) ? "edr" : ftp2ext(ftp));
if (debug)
{
fprintf(debug, "rank %d par_fn '%s'\n", cr->nodeid, buf);
if (fn2ftp(buf) == efLOG)
{
fprintf(debug, "log\n");
}
}
}
static void par_fn(char *base,int ftp,const t_commrec *cr,
bool bUnderScore,
char buf[],int bufsize)
{
int n;
if(bufsize<(strlen(base)+4))
gmx_mem("Character buffer too small!");
/* Copy to buf, and strip extension */
strcpy(buf,base);
buf[strlen(base) - strlen(ftp2ext(fn2ftp(base))) - 1] = '\0';
/* Add node info */
if (bUnderScore)
strcat(buf,"_");
if (MULTISIM(cr) && !bUnderScore) {
sprintf(buf+strlen(buf),"%d",cr->ms->sim);
} else if (PAR(cr)) {
sprintf(buf+strlen(buf),"%d",cr->nodeid);
}
strcat(buf,".");
/* Add extension again */
strcat(buf,(ftp == efTPX) ? "tpr" : (ftp == efEDR) ? "edr" : ftp2ext(ftp));
}
static void read_stx_conf(const char *infile, t_topology *top,
rvec x[], rvec *v, int *ePBC, matrix box)
{
FILE *in;
t_trxframe fr;
int ftp;
char g96_line[STRLEN+1];
if (top->atoms.nr == 0)
{
fprintf(stderr, "Warning: Number of atoms in %s is 0\n", infile);
}
else if (top->atoms.atom == NULL)
{
gmx_mem("Uninitialized array atom");
}
if (ePBC)
{
*ePBC = -1;
}
ftp = fn2ftp(infile);
switch (ftp)
{
case efGRO:
gmx_gro_read_conf(infile, top, x, v, box);
break;
case efG96:
fr.title = NULL;
fr.natoms = top->atoms.nr;
fr.atoms = &top->atoms;
fr.x = x;
fr.v = v;
fr.f = NULL;
in = gmx_fio_fopen(infile, "r");
read_g96_conf(in, infile, &fr, &top->symtab, g96_line);
gmx_fio_fclose(in);
copy_mat(fr.box, box);
top->name = put_symtab(&top->symtab, fr.title);
sfree(const_cast<char *>(fr.title));
break;
case efPDB:
case efBRK:
case efENT:
gmx_pdb_read_conf(infile, top, x, ePBC, box);
break;
case efESP:
gmx_espresso_read_conf(infile, top, x, v, box);
break;
default:
gmx_incons("Not supported in read_stx_conf");
}
}
void read_stx_conf(const char *infile, char *title, t_atoms *atoms,
rvec x[], rvec *v, int *ePBC, matrix box)
{
FILE *in;
char buf[256];
gmx_mtop_t *mtop;
t_topology top;
t_trxframe fr;
int i, ftp, natoms;
real d;
char g96_line[STRLEN+1];
if (atoms->nr == 0)
{
fprintf(stderr, "Warning: Number of atoms in %s is 0\n", infile);
}
else if (atoms->atom == NULL)
{
gmx_mem("Uninitialized array atom");
}
if (ePBC)
{
*ePBC = -1;
}
ftp = fn2ftp(infile);
switch (ftp)
{
case efGRO:
read_whole_conf(infile, title, atoms, x, v, box);
break;
case efG96:
fr.title = NULL;
fr.natoms = atoms->nr;
fr.atoms = atoms;
fr.x = x;
fr.v = v;
fr.f = NULL;
in = gmx_fio_fopen(infile, "r");
read_g96_conf(in, infile, &fr, g96_line);
gmx_fio_fclose(in);
copy_mat(fr.box, box);
strncpy(title, fr.title, STRLEN);
break;
case efPDB:
case efBRK:
case efENT:
read_pdb_conf(infile, title, atoms, x, ePBC, box, TRUE, NULL);
break;
case efESP:
read_espresso_conf(infile, atoms, x, v, box);
break;
case efTPR:
case efTPB:
case efTPA:
snew(mtop, 1);
i = read_tpx(infile, NULL, box, &natoms, x, v, NULL, mtop);
if (ePBC)
{
*ePBC = i;
}
strcpy(title, *(mtop->name));
/* Free possibly allocated memory */
done_atom(atoms);
*atoms = gmx_mtop_global_atoms(mtop);
top = gmx_mtop_t_to_t_topology(mtop);
tpx_make_chain_identifiers(atoms, &top.mols);
sfree(mtop);
/* The strings in the symtab are still in use in the returned t_atoms
* structure, so we should not free them. But there is no place to put the
* symbols; the only choice is to leak the memory...
* So we clear the symbol table before freeing the topology structure. */
free_symtab(&top.symtab);
done_top(&top);
break;
default:
gmx_incons("Not supported in read_stx_conf");
}
}
void read_stx_conf(char *infile, char *title,t_atoms *atoms,
rvec x[],rvec *v,int *ePBC,matrix box)
{
FILE *in;
char buf[256];
gmx_mtop_t *mtop;
t_topology top;
t_trxframe fr;
int i,ftp,natoms,i1;
real d,r1,r2;
if (atoms->nr == 0)
fprintf(stderr,"Warning: Number of atoms in %s is 0\n",infile);
else if (atoms->atom == NULL)
gmx_mem("Uninitialized array atom");
if (ePBC)
*ePBC = -1;
ftp=fn2ftp(infile);
switch (ftp) {
case efGRO:
read_whole_conf(infile, title, atoms, x, v, box);
break;
case efG96:
fr.title = title;
fr.natoms = atoms->nr;
fr.atoms = atoms;
fr.x = x;
fr.v = v;
fr.f = NULL;
in = gmx_fio_fopen(infile,"r");
read_g96_conf(in, infile, &fr);
gmx_fio_fclose(in);
copy_mat(fr.box,box);
break;
case efPDB:
case efBRK:
case efENT:
read_pdb_conf(infile, title, atoms, x, ePBC, box, TRUE, NULL);
break;
case efESP:
read_espresso_conf(infile,atoms,x,v,box);
break;
case efTPR:
case efTPB:
case efTPA:
snew(mtop,1);
i = read_tpx(infile,&i1,&r1,&r2,NULL,box,&natoms,x,v,NULL,mtop);
if (ePBC)
*ePBC = i;
strcpy(title,*(mtop->name));
/* Free possibly allocated memory */
done_atom(atoms);
*atoms = gmx_mtop_global_atoms(mtop);
top = gmx_mtop_t_to_t_topology(mtop);
tpx_make_chain_identifiers(atoms,&top.mols);
sfree(mtop);
done_top(&top);
break;
default:
gmx_incons("Not supported in read_stx_conf");
}
}
