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 init_parallel(FILE *log,char *tpxfile,t_commrec *cr,
t_inputrec *inputrec,gmx_mtop_t *mtop,
t_state *state,
int list)
{
int step;
real t;
char buf[256];
if (MASTER(cr)) {
init_inputrec(inputrec);
read_tpx_state(tpxfile,&step,&t,inputrec,state,NULL,mtop);
/* When we will be doing domain decomposition with separate PME nodes
* the rng entries will be too large, we correct for this later.
*/
set_state_entries(state,inputrec,cr->nnodes);
}
bcast_ir_mtop(cr,inputrec,mtop);
if (inputrec->eI == eiBD || EI_SD(inputrec->eI)) {
/* Make sure the random seeds are different on each node */
inputrec->ld_seed += cr->nodeid;
}
/* Printing */
if (list!=0 && log!=NULL)
{
if (list&LIST_INPUTREC)
pr_inputrec(log,0,"parameters of the run",inputrec,FALSE);
if (list&LIST_X)
pr_rvecs(log,0,"box",state->box,DIM);
if (list&LIST_X)
pr_rvecs(log,0,"box_rel",state->box_rel,DIM);
if (list&LIST_V)
pr_rvecs(log,0,"boxv",state->boxv,DIM);
if (list&LIST_X)
pr_rvecs(log,0,int_title("x",0,buf,255),state->x,state->natoms);
if (list&LIST_V)
pr_rvecs(log,0,int_title("v",0,buf,255),state->v,state->natoms);
if (list&LIST_TOP)
pr_mtop(log,0,int_title("topology",cr->nodeid,buf,255),mtop,TRUE);
fflush(log);
}
}
void test3() {
const char *fn = "../state0.cpt";
FILE *fplog = stderr;
t_commrec cr;
gmx_bool bPartDecomp = FALSE;
ivec dd_nc;
t_inputrec ir;
t_state state;
gmx_bool
bReadRNG = TRUE,
bReadEkin = TRUE,
bAppend = TRUE,
bForceAppend = FALSE;
init_state(&state, -1,-1,-1,-1);
init_inputrec(&ir);
int simulation_part;
gmx_large_int_t step;
double t;
read_checkpoint_state(fn, &simulation_part,
&step, &t, &state);
/* load_checkpoint(fn, &fplog, */
/* &cr, bPartDecomp, dd_nc, */
/* &ir, &state, */
/* &bReadRNG, &bReadEkin, */
/* bAppend, bForceAppend); */
printf("%u\n", *state.ld_rng);
}
// 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); */
}
