tpr_t * guamps_init_tpr(const int natoms) {
tpr_t *tpr = (tpr_t *)calloc(1, sizeof(tpr_t));
tpr->natoms = natoms;
init_inputrec (&tpr->inputrec);
init_state (&tpr->state, -1,-1,-1,-1);
tpr->f = (rvec *)calloc(natoms, sizeof(rvec));
init_mtop (&tpr->mtop);
return tpr;
}
void do_nsgrid(FILE *fp, gmx_bool bVerbose,
matrix box, rvec x[], t_atoms *atoms, real rlong,
const output_env_t oenv)
{
gmx_mtop_t *mtop;
gmx_localtop_t *top;
t_mdatoms *md;
t_block *cgs;
t_inputrec *ir;
t_nrnb nrnb;
t_commrec *cr;
int *cg_index;
gmx_moltype_t *molt;
gmx_ffparams_t *ffp;
ivec *nFreeze;
int i, m, natoms;
rvec box_size;
real *lambda, *dvdl;
natoms = atoms->nr;
/* Charge group index */
snew(cg_index, natoms);
for (i = 0; (i < natoms); i++)
{
cg_index[i] = i;
}
/* Topology needs charge groups and exclusions */
snew(mtop, 1);
init_mtop(mtop);
mtop->natoms = natoms;
/* Make one moltype that contains the whol system */
mtop->nmoltype = 1;
snew(mtop->moltype, mtop->nmoltype);
molt = &mtop->moltype[0];
molt->name = mtop->name;
molt->atoms = *atoms;
stupid_fill_block(&molt->cgs, mtop->natoms, FALSE);
stupid_fill_blocka(&molt->excls, natoms);
/* Make one molblock for the whole system */
mtop->nmolblock = 1;
snew(mtop->molblock, mtop->nmolblock);
mtop->molblock[0].type = 0;
mtop->molblock[0].nmol = 1;
mtop->molblock[0].natoms_mol = natoms;
/* Initialize a single energy group */
mtop->groups.grps[egcENER].nr = 1;
mtop->groups.ngrpnr[egcENER] = 0;
mtop->groups.grpnr[egcENER] = NULL;
ffp = &mtop->ffparams;
ffp->ntypes = 1;
ffp->atnr = 1;
ffp->reppow = 12;
snew(ffp->functype, 1);
snew(ffp->iparams, 1);
ffp->iparams[0].lj.c6 = 1;
ffp->iparams[0].lj.c12 = 1;
/* inputrec structure */
snew(ir, 1);
ir->coulombtype = eelCUT;
ir->vdwtype = evdwCUT;
ir->ndelta = 2;
ir->ns_type = ensGRID;
snew(ir->opts.egp_flags, 1);
top = gmx_mtop_generate_local_top(mtop, ir);
/* Some nasty shortcuts */
cgs = &(top->cgs);
/* mdatoms structure */
snew(nFreeze, 2);
snew(md, 1);
md = init_mdatoms(fp, mtop, FALSE);
atoms2md(mtop, ir, 0, NULL, 0, mtop->natoms, md);
sfree(nFreeze);
/* forcerec structure */
if (fr == NULL)
{
fr = mk_forcerec();
}
snew(cr, 1);
cr->nnodes = 1;
/* cr->nthreads = 1; */
/* ir->rlist = ir->rcoulomb = ir->rvdw = rlong;
printf("Neighborsearching with a cut-off of %g\n",rlong);
init_forcerec(stdout,fr,ir,top,cr,md,box,FALSE,NULL,NULL,NULL,TRUE);*/
fr->cg0 = 0;
fr->hcg = top->cgs.nr;
fr->nWatMol = 0;
/* Prepare for neighboursearching */
init_nrnb(&nrnb);
/* Init things dependent on parameters */
ir->rlistlong = ir->rlist = ir->rcoulomb = ir->rvdw = rlong;
/* create free energy data to avoid NULLs */
snew(ir->fepvals, 1);
printf("Neighborsearching with a cut-off of %g\n", rlong);
init_forcerec(stdout, oenv, fr, NULL, ir, mtop, cr, box, FALSE,
NULL, NULL, NULL, NULL, NULL, TRUE, -1);
if (debug)
{
pr_forcerec(debug, fr, cr);
}
/* Calculate new stuff dependent on coords and box */
for (m = 0; (m < DIM); m++)
{
box_size[m] = box[m][m];
}
calc_shifts(box, fr->shift_vec);
put_charge_groups_in_box(fp, 0, cgs->nr, fr->ePBC, box, cgs, x, fr->cg_cm);
/* Do the actual neighboursearching */
snew(lambda, efptNR);
snew(dvdl, efptNR);
init_neighbor_list(fp, fr, md->homenr);
search_neighbours(fp, fr, x, box, top,
&mtop->groups, cr, &nrnb, md, lambda, dvdl, NULL, TRUE, FALSE, FALSE);
if (debug)
{
dump_nblist(debug, cr, fr, 0);
}
if (bVerbose)
{
fprintf(stderr, "Successfully made neighbourlist\n");
}
}
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;
}
// works
void test1() {
const char
*intopol = "../topol.tpr",
*incpt = "../state0.cpt",
*outtopol = "../new.tpr";
const unsigned int seed = 42;
// read the header
t_tpxheader header;
int version, generation;
read_tpxheader(intopol, &header, FALSE, &version, &generation);
// decide if forces can be read from tpr
rvec *forces;
if (header.bF) {
snew(forces, 1);
} else {
forces = NULL;
}
// read the topology file
t_inputrec ir;
t_state topol_state;
gmx_mtop_t mtop;
init_inputrec(&ir);
init_state(&topol_state, -1, -1, -1, -1);
init_mtop(&mtop);
read_tpx_state(intopol,
&ir, &topol_state, forces,
&mtop);
// read the checkpoint
int sim_part;
gmx_large_int_t step;
double time;
t_state cpt_state;
t_commrec comm;
init_state(&cpt_state, -1, -1, -1, -1);
printf("Opening %s for reading\n", incpt);
read_checkpoint_state(incpt, &sim_part, &step, &time, &cpt_state);
printf("ld_rng = %d\n", (int) cpt_state.ld_rng);
printf("ld_rngi = %d\n" , (int) cpt_state.ld_rngi);
// update the state to be written
/* gmx_rng_t rng = gmx_rng_init(seed); */
/* unsigned int rng_state, rng_index; */
/* gmx_rng_get_state(rng, &rng_state, &rng_index); */
ir.ld_seed = 42;
ir.init_t = time;
ir.init_step = step;
ir.init_lambda = cpt_state.lambda;
/* // write the new tpr */
/* write_tpx_state(outtopol, */
/* &ir, &cpt_state, &mtop); */
}
