int
main(int argc, char *argv[])
{
int ret = EXIT_FAILURE;
virConnectPtr conn = NULL;
const char *uri = NULL;
const char *dom_name = NULL;
unsigned int milliseconds = 500; /* Sleep this long between two API calls */
const int connect_flags = 0; /* No connect flags for now */
parse_argv(argc, argv, &uri, &dom_name, &milliseconds);
DEBUG("Proceeding with uri=%s dom_name=%s milliseconds=%u",
uri, dom_name, milliseconds);
if (!(conn = virConnectOpenAuth(uri,
virConnectAuthPtrDefault,
connect_flags))) {
ERROR("Failed to connect to hypervisor");
goto cleanup;
}
DEBUG("Successfully connected");
if (!dom_name) {
if (fetch_domains(conn) == 0)
ret = EXIT_SUCCESS;
goto cleanup;
}
if (do_top(conn, dom_name, milliseconds) < 0)
goto cleanup;
ret = EXIT_SUCCESS;
cleanup:
if (conn) {
int tmp;
tmp = virConnectClose(conn);
if (tmp < 0) {
ERROR("Failed to disconnect from the hypervisor");
ret = EXIT_FAILURE;
} else if (tmp > 0) {
ERROR("One or more references were leaked after "
"disconnect from the hypervisor");
ret = EXIT_FAILURE;
} else {
DEBUG("Connection successfully closed");
}
}
return ret;
}
static void
new_status(char *topfile,char *topppfile,char *confin,
t_gromppopts *opts,t_inputrec *ir,bool bZero,
bool bGenVel,bool bVerbose,t_state *state,
gpp_atomtype_t atype,gmx_mtop_t *sys,
int *nmi,t_molinfo **mi,t_params plist[],
int *comb,double *reppow,real *fudgeQQ,
bool bMorse,
int *nerror)
{
t_molinfo *molinfo=NULL;
int nmolblock;
gmx_molblock_t *molblock,*molbs;
t_atoms *confat;
int mb,mbs,i,nrmols,nmismatch;
char buf[STRLEN];
bool bGB=FALSE;
init_mtop(sys);
/* Set boolean for GB */
if(ir->implicit_solvent)
bGB=TRUE;
/* TOPOLOGY processing */
sys->name = do_top(bVerbose,topfile,topppfile,opts,bZero,&(sys->symtab),
plist,comb,reppow,fudgeQQ,
atype,&nrmols,&molinfo,ir,
&nmolblock,&molblock,bGB);
sys->nmolblock = 0;
snew(sys->molblock,nmolblock);
mbs;
sys->natoms = 0;
for(mb=0; mb<nmolblock; mb++) {
if (sys->nmolblock > 0 &&
molblock[mb].type == sys->molblock[sys->nmolblock-1].type) {
/* Merge consecutive blocks with the same molecule type */
sys->molblock[sys->nmolblock-1].nmol += molblock[mb].nmol;
sys->natoms += molblock[mb].nmol*sys->molblock[sys->nmolblock-1].natoms_mol;
} else if (molblock[mb].nmol > 0) {
/* Add a new molblock to the topology */
molbs = &sys->molblock[sys->nmolblock];
*molbs = molblock[mb];
molbs->natoms_mol = molinfo[molbs->type].atoms.nr;
molbs->nposres_xA = 0;
molbs->nposres_xB = 0;
sys->natoms += molbs->nmol*molbs->natoms_mol;
sys->nmolblock++;
}
}
if (sys->nmolblock == 0) {
gmx_fatal(FARGS,"No molecules were defined in the system");
}
renumber_moltypes(sys,&nrmols,&molinfo);
if (bMorse)
convert_harmonics(nrmols,molinfo,atype);
if (ir->eDisre == edrNone) {
i = rm_interactions(F_DISRES,nrmols,molinfo);
if (i > 0) {
set_warning_line("unknown",-1);
sprintf(warn_buf,"disre = no, removed %d distance restraints",i);
warning_note(NULL);
}
}
if (opts->bOrire == FALSE) {
i = rm_interactions(F_ORIRES,nrmols,molinfo);
if (i > 0) {
set_warning_line("unknown",-1);
sprintf(warn_buf,"orire = no, removed %d orientation restraints",i);
warning_note(NULL);
}
}
if (opts->bDihre == FALSE) {
i = rm_interactions(F_DIHRES,nrmols,molinfo);
if (i > 0) {
set_warning_line("unknown",-1);
sprintf(warn_buf,"dihre = no, removed %d dihedral restraints",i);
warning_note(NULL);
}
}
/* Copy structures from msys to sys */
molinfo2mtop(nrmols,molinfo,sys);
/* COORDINATE file processing */
if (bVerbose)
fprintf(stderr,"processing coordinates...\n");
get_stx_coordnum(confin,&state->natoms);
if (state->natoms != sys->natoms)
gmx_fatal(FARGS,"number of coordinates in coordinate file (%s, %d)\n"
" does not match topology (%s, %d)",
confin,state->natoms,topfile,sys->natoms);
else {
/* make space for coordinates and velocities */
char title[STRLEN];
snew(confat,1);
init_t_atoms(confat,state->natoms,FALSE);
init_state(state,state->natoms,0);
read_stx_conf(confin,title,confat,state->x,state->v,NULL,state->box);
/* This call fixes the box shape for runs with pressure scaling */
set_box_rel(ir,state);
nmismatch = check_atom_names(topfile, confin, sys, confat);
free_t_atoms(confat,TRUE);
sfree(confat);
if (nmismatch) {
sprintf(buf,"%d non-matching atom name%s\n"
"atom names from %s will be used\n"
"atom names from %s will be ignored\n",
nmismatch,(nmismatch == 1) ? "" : "s",topfile,confin);
warning(buf);
}
if (bVerbose)
fprintf(stderr,"double-checking input for internal consistency...\n");
double_check(ir,state->box,nint_ftype(sys,molinfo,F_CONSTR),nerror);
}
if (bGenVel) {
real *mass;
gmx_mtop_atomloop_all_t aloop;
t_atom *atom;
snew(mass,state->natoms);
aloop = gmx_mtop_atomloop_all_init(sys);
while (gmx_mtop_atomloop_all_next(aloop,&i,&atom)) {
mass[i] = atom->m;
}
if (opts->seed == -1) {
opts->seed = make_seed();
fprintf(stderr,"Setting gen_seed to %d\n",opts->seed);
}
maxwell_speed(opts->tempi,opts->seed,sys,state->v);
stop_cm(stdout,state->natoms,mass,state->x,state->v);
sfree(mass);
}
*nmi = nrmols;
*mi = molinfo;
}
