int write_traj(FILE *log,t_commrec *cr,
char *traj,t_nsborder *nsb,
int step,real t,real lambda,t_nrnb nrnb[],
int natoms,rvec *xx,rvec *vv,rvec *ff,matrix box)
{
static int fp=-1;
if ((fp == -1) && MASTER(cr)) {
#ifdef DEBUG
fprintf(log,"Going to open trajectory file: %s\n",traj);
#endif
fp = open_trn(traj,"w");
}
#define MX(xvf) moveit(log,cr->left,cr->right,#xvf,xvf,nsb)
if (cr->nnodes > 1) {
MX(xx);
MX(vv);
MX(ff);
}
if ((xx || vv || ff) && MASTER(cr)) {
fwrite_trn(fp,step,t,lambda,box,natoms,xx,vv,ff);
gmx_fio_flush(fp);
}
return fp;
}
int write_xtc(int fp,
int natoms,int step,real time,
matrix box,rvec *x,real prec)
{
int magic_number = XTC_MAGIC;
XDR *xd;
bool bDum;
int bOK;
xd = gmx_fio_getxdr(fp);
/* write magic number and xtc identidier */
if (xtc_header(xd,&magic_number,&natoms,&step,&time,FALSE,&bDum) == 0)
{
return 0;
}
/* write data */
bOK = xtc_coord(xd,&natoms,box,x,&prec,FALSE); /* bOK will be 1 if writing went well */
if(bOK)
{
if(gmx_fio_flush(fp) !=0)
{
bOK = 0;
}
}
return bOK; /* 0 if bad, 1 if writing went well */
}
int
gmx_fio_get_output_file_positions(gmx_file_position_t **p_outputfiles, int *p_nfiles)
{
int i,nfiles,rc,nalloc;
int pos_hi,pos_lo;
long pos;
gmx_file_position_t * outputfiles;
char buf[STRLEN];
nfiles = 0;
nalloc = 100;
snew(outputfiles,nalloc);
for(i=0; i<nFIO; i++)
{
/* Skip the checkpoint files themselves, since they could be open when we call this routine... */
if(FIO[i].bOpen && !FIO[i].bRead && !FIO[i].bStdio && FIO[i].iFTP!=efCPT)
{
/* This is an output file currently open for writing, add it */
if(nfiles == nalloc)
{
nalloc += 100;
srenew(outputfiles,nalloc);
}
strncpy(outputfiles[nfiles].filename,FIO[i].fn,STRLEN-1);
/* Flush the file, so we are sure it is written */
if (gmx_fio_flush(i) != 0)
{
sprintf(buf,"Cannot write file '%s'; maybe you are out of disk space or quota?",FIO[i].fn);
gmx_file(buf);
}
/* We cannot count on XDR being able to write 64-bit integers, so separate into high/low 32-bit values.
* In case the filesystem has 128-bit offsets we only care about the first 64 bits - we'll have to fix
* this when exabyte-size output files are common...
*/
#ifdef HAVE_FSEEKO
outputfiles[nfiles].offset = ftello(FIO[i].fp);
#else
outputfiles[nfiles].offset = ftell(FIO[i].fp);
#endif
nfiles++;
}
}
*p_nfiles = nfiles;
*p_outputfiles = outputfiles;
return 0;
}
int write_xtc(t_fileio *fio,
int natoms, int64_t step, real time,
const rvec *box, const rvec *x, real prec)
{
int magic_number = XTC_MAGIC;
XDR *xd;
gmx_bool bDum;
int bOK;
if (!fio)
{
/* This means the fio object is not being used, e.g. because
we are actually writing TNG output. We still have to return
a pseudo-success value, to keep some callers happy. */
return 1;
}
xd = gmx_fio_getxdr(fio);
/* write magic number and xtc identidier */
if (xtc_header(xd, &magic_number, &natoms, &step, &time, FALSE, &bDum) == 0)
{
return 0;
}
/* write data */
bOK = xtc_coord(xd, &natoms, const_cast<rvec *>(box), const_cast<rvec *>(x), &prec, FALSE); /* bOK will be 1 if writing went well */
if (bOK)
{
if (gmx_fio_flush(fio) != 0)
{
bOK = 0;
}
}
return bOK; /* 0 if bad, 1 if writing went well */
}
void mdoutf_write_to_trajectory_files(FILE *fplog, t_commrec *cr,
gmx_mdoutf_t of,
int mdof_flags,
gmx_mtop_t *top_global,
gmx_int64_t step, double t,
t_state *state_local, t_state *state_global,
rvec *f_local, rvec *f_global)
{
rvec *local_v;
rvec *global_v;
/* MRS -- defining these variables is to manage the difference
* between half step and full step velocities, but there must be a better way . . . */
local_v = state_local->v;
global_v = state_global->v;
if (DOMAINDECOMP(cr))
{
if (mdof_flags & MDOF_CPT)
{
dd_collect_state(cr->dd, state_local, state_global);
}
else
{
if (mdof_flags & (MDOF_X | MDOF_X_COMPRESSED))
{
dd_collect_vec(cr->dd, state_local, state_local->x,
state_global->x);
}
if (mdof_flags & MDOF_V)
{
dd_collect_vec(cr->dd, state_local, local_v,
global_v);
}
}
if (mdof_flags & MDOF_F)
{
dd_collect_vec(cr->dd, state_local, f_local, f_global);
}
}
else
{
if (mdof_flags & MDOF_CPT)
{
/* All pointers in state_local are equal to state_global,
* but we need to copy the non-pointer entries.
*/
state_global->lambda = state_local->lambda;
state_global->veta = state_local->veta;
state_global->vol0 = state_local->vol0;
copy_mat(state_local->box, state_global->box);
copy_mat(state_local->boxv, state_global->boxv);
copy_mat(state_local->svir_prev, state_global->svir_prev);
copy_mat(state_local->fvir_prev, state_global->fvir_prev);
copy_mat(state_local->pres_prev, state_global->pres_prev);
}
}
if (MASTER(cr))
{
if (mdof_flags & MDOF_CPT)
{
fflush_tng(of->tng);
fflush_tng(of->tng_low_prec);
write_checkpoint(of->fn_cpt, of->bKeepAndNumCPT,
fplog, cr, of->eIntegrator, of->simulation_part,
of->bExpanded, of->elamstats, step, t, state_global);
}
if (mdof_flags & (MDOF_X | MDOF_V | MDOF_F))
{
if (of->fp_trn)
{
gmx_trr_write_frame(of->fp_trn, step, t, state_local->lambda[efptFEP],
state_local->box, top_global->natoms,
(mdof_flags & MDOF_X) ? state_global->x : NULL,
(mdof_flags & MDOF_V) ? global_v : NULL,
(mdof_flags & MDOF_F) ? f_global : NULL);
if (gmx_fio_flush(of->fp_trn) != 0)
{
gmx_file("Cannot write trajectory; maybe you are out of disk space?");
}
}
gmx_fwrite_tng(of->tng, FALSE, step, t, state_local->lambda[efptFEP],
state_local->box,
top_global->natoms,
(mdof_flags & MDOF_X) ? state_global->x : NULL,
(mdof_flags & MDOF_V) ? global_v : NULL,
(mdof_flags & MDOF_F) ? f_global : NULL);
}
if (mdof_flags & MDOF_X_COMPRESSED)
{
rvec *xxtc = NULL;
if (of->natoms_x_compressed == of->natoms_global)
{
/* We are writing the positions of all of the atoms to
the compressed output */
xxtc = state_global->x;
}
else
{
/* We are writing the positions of only a subset of
the atoms to the compressed output, so we have to
make a copy of the subset of coordinates. */
int i, j;
snew(xxtc, of->natoms_x_compressed);
for (i = 0, j = 0; (i < of->natoms_global); i++)
{
if (ggrpnr(of->groups, egcCompressedX, i) == 0)
{
copy_rvec(state_global->x[i], xxtc[j++]);
}
}
}
if (write_xtc(of->fp_xtc, of->natoms_x_compressed, step, t,
state_local->box, xxtc, of->x_compression_precision) == 0)
{
gmx_fatal(FARGS, "XTC error - maybe you are out of disk space?");
}
gmx_fwrite_tng(of->tng_low_prec,
TRUE,
step,
t,
state_local->lambda[efptFEP],
state_local->box,
of->natoms_x_compressed,
xxtc,
NULL,
NULL);
if (of->natoms_x_compressed != of->natoms_global)
{
sfree(xxtc);
}
}
}
}
gmx_bool do_enx(ener_file_t ef,t_enxframe *fr)
{
int file_version=-1;
int i,b;
gmx_bool bRead,bOK,bOK1,bSane;
real tmp1,tmp2,rdum;
char buf[22];
/*int d_size;*/
bOK = TRUE;
bRead = gmx_fio_getread(ef->fio);
if (!bRead)
{
fr->e_size = fr->nre*sizeof(fr->ener[0].e)*4;
/*d_size = fr->ndisre*(sizeof(real)*2);*/
}
gmx_fio_checktype(ef->fio);
if (!do_eheader(ef,&file_version,fr,-1,NULL,&bOK))
{
if (bRead)
{
fprintf(stderr,"\rLast energy frame read %d time %8.3f ",
ef->framenr-1,ef->frametime);
if (!bOK)
{
fprintf(stderr,
"\nWARNING: Incomplete energy frame: nr %d time %8.3f\n",
ef->framenr,fr->t);
}
}
else
{
gmx_file("Cannot write energy file header; maybe you are out of quota?");
}
return FALSE;
}
if (bRead)
{
if ((ef->framenr < 20 || ef->framenr % 10 == 0) &&
(ef->framenr < 200 || ef->framenr % 100 == 0) &&
(ef->framenr < 2000 || ef->framenr % 1000 == 0))
{
fprintf(stderr,"\rReading energy frame %6d time %8.3f ",
ef->framenr,fr->t);
}
ef->framenr++;
ef->frametime = fr->t;
}
/* Check sanity of this header */
bSane = fr->nre > 0 ;
for(b=0; b<fr->nblock; b++)
{
bSane = bSane || (fr->block[b].nsub > 0);
}
if (!((fr->step >= 0) && bSane))
{
fprintf(stderr,"\nWARNING: there may be something wrong with energy file %s\n",
gmx_fio_getname(ef->fio));
fprintf(stderr,"Found: step=%s, nre=%d, nblock=%d, time=%g.\n"
"Trying to skip frame expect a crash though\n",
gmx_step_str(fr->step,buf),fr->nre,fr->nblock,fr->t);
}
if (bRead && fr->nre > fr->e_alloc)
{
srenew(fr->ener,fr->nre);
for(i=fr->e_alloc; (i<fr->nre); i++)
{
fr->ener[i].e = 0;
fr->ener[i].eav = 0;
fr->ener[i].esum = 0;
}
fr->e_alloc = fr->nre;
}
for(i=0; i<fr->nre; i++)
{
bOK = bOK && gmx_fio_do_real(ef->fio, fr->ener[i].e);
/* Do not store sums of length 1,
* since this does not add information.
*/
if (file_version == 1 ||
(bRead && fr->nsum > 0) || fr->nsum > 1)
{
tmp1 = fr->ener[i].eav;
bOK = bOK && gmx_fio_do_real(ef->fio, tmp1);
if (bRead)
fr->ener[i].eav = tmp1;
/* This is to save only in single precision (unless compiled in DP) */
tmp2 = fr->ener[i].esum;
bOK = bOK && gmx_fio_do_real(ef->fio, tmp2);
if (bRead)
fr->ener[i].esum = tmp2;
if (file_version == 1)
{
/* Old, unused real */
rdum = 0;
bOK = bOK && gmx_fio_do_real(ef->fio, rdum);
}
}
}
/* Here we can not check for file_version==1, since one could have
* continued an old format simulation with a new one with mdrun -append.
*/
if (bRead && ef->eo.bOldFileOpen)
{
/* Convert old full simulation sums to sums between energy frames */
convert_full_sums(&(ef->eo),fr);
}
/* read the blocks */
for(b=0; b<fr->nblock; b++)
{
/* now read the subblocks. */
int nsub=fr->block[b].nsub; /* shortcut */
int i;
for(i=0;i<nsub;i++)
{
t_enxsubblock *sub=&(fr->block[b].sub[i]); /* shortcut */
if (bRead)
{
enxsubblock_alloc(sub);
}
/* read/write data */
bOK1=TRUE;
switch (sub->type)
{
case xdr_datatype_float:
bOK1=gmx_fio_ndo_float(ef->fio, sub->fval, sub->nr);
break;
case xdr_datatype_double:
bOK1=gmx_fio_ndo_double(ef->fio, sub->dval, sub->nr);
break;
case xdr_datatype_int:
bOK1=gmx_fio_ndo_int(ef->fio, sub->ival, sub->nr);
break;
case xdr_datatype_large_int:
bOK1=gmx_fio_ndo_gmx_large_int(ef->fio, sub->lval, sub->nr);
break;
case xdr_datatype_char:
bOK1=gmx_fio_ndo_uchar(ef->fio, sub->cval, sub->nr);
break;
case xdr_datatype_string:
bOK1=gmx_fio_ndo_string(ef->fio, sub->sval, sub->nr);
break;
default:
gmx_incons("Reading unknown block data type: this file is corrupted or from the future");
}
bOK = bOK && bOK1;
}
}
if(!bRead)
{
if( gmx_fio_flush(ef->fio) != 0)
{
gmx_file("Cannot write energy file; maybe you are out of quota?");
}
}
if (!bOK)
{
if (bRead)
{
fprintf(stderr,"\nLast energy frame read %d",
ef->framenr-1);
fprintf(stderr,"\nWARNING: Incomplete energy frame: nr %d time %8.3f\n",
ef->framenr,fr->t);
}
else
{
gmx_fatal(FARGS,"could not write energies");
}
return FALSE;
}
return TRUE;
}
bool do_enx(int fp,t_enxframe *fr)
{
int file_version=-1;
int i,block;
bool bRead,bOK,bOK1,bSane;
real tmp1,tmp2,rdum;
char buf[22];
bOK = TRUE;
bRead = gmx_fio_getread(fp);
if (!bRead)
{
fr->e_size = fr->nre*sizeof(fr->ener[0].e)*4;
fr->d_size = fr->ndisre*(sizeof(fr->disre_rm3tav[0]) +
sizeof(fr->disre_rt[0]));
}
gmx_fio_select(fp);
if (!do_eheader(fp,&file_version,fr,FALSE,&bOK))
{
if (bRead)
{
fprintf(stderr,"\rLast energy frame read %d time %8.3f ",
framenr-1,frametime);
if (!bOK)
{
fprintf(stderr,
"\nWARNING: Incomplete energy frame: nr %d time %8.3f\n",
framenr,fr->t);
}
}
else
{
gmx_file("Cannot write energy file header; maybe you are out of quota?");
}
return FALSE;
}
if (bRead)
{
if ((framenr < 20 || framenr % 10 == 0) &&
(framenr < 200 || framenr % 100 == 0) &&
(framenr < 2000 || framenr % 1000 == 0))
{
fprintf(stderr,"\rReading energy frame %6d time %8.3f ",
framenr,fr->t);
}
framenr++;
frametime = fr->t;
}
/* Check sanity of this header */
bSane = (fr->nre > 0 || fr->ndisre > 0);
for(block=0; block<fr->nblock; block++)
{
bSane = bSane || (fr->nr[block] > 0);
}
if (!((fr->step >= 0) && bSane))
{
fprintf(stderr,"\nWARNING: there may be something wrong with energy file %s\n",
gmx_fio_getname(fp));
fprintf(stderr,"Found: step=%s, nre=%d, ndisre=%d, nblock=%d, time=%g.\n"
"Trying to skip frame expect a crash though\n",
gmx_step_str(fr->step,buf),fr->nre,fr->ndisre,fr->nblock,fr->t);
}
if (bRead && fr->nre > fr->e_alloc)
{
srenew(fr->ener,fr->nre);
for(i=fr->e_alloc; (i<fr->nre); i++)
{
fr->ener[i].e = 0;
fr->ener[i].eav = 0;
fr->ener[i].esum = 0;
}
fr->e_alloc = fr->nre;
}
for(i=0; i<fr->nre; i++)
{
bOK = bOK && do_real(fr->ener[i].e);
/* Do not store sums of length 1,
* since this does not add information.
*/
if (file_version == 1 ||
(bRead && fr->nsum > 0) || fr->nsum > 1)
{
tmp1 = fr->ener[i].eav;
bOK = bOK && do_real(tmp1);
if (bRead)
fr->ener[i].eav = tmp1;
/* This is to save only in single precision (unless compiled in DP) */
tmp2 = fr->ener[i].esum;
bOK = bOK && do_real(tmp2);
if (bRead)
fr->ener[i].esum = tmp2;
if (file_version == 1)
{
/* Old, unused real */
rdum = 0;
bOK = bOK && do_real(rdum);
}
}
}
/* Here we can not check for file_version==1, since one could have
* continued an old format simulation with a new one with mdrun -append.
*/
if (bRead && fp < ener_old_nalloc && ener_old[fp].bOldFileOpen)
{
/* Convert old full simulation sums to sums between energy frames */
convert_full_sums(&ener_old[fp],fr);
}
if (fr->ndisre)
{
if (bRead && fr->ndisre>fr->d_alloc)
{
srenew(fr->disre_rm3tav,fr->ndisre);
srenew(fr->disre_rt,fr->ndisre);
fr->d_alloc = fr->ndisre;
}
ndo_real(fr->disre_rm3tav,fr->ndisre,bOK1);
bOK = bOK && bOK1;
ndo_real(fr->disre_rt,fr->ndisre,bOK1);
bOK = bOK && bOK1;
}
for(block=0; block<fr->nblock; block++)
{
if (bRead && fr->nr[block]>fr->b_alloc[block])
{
srenew(fr->block[block],fr->nr[block]);
fr->b_alloc[block] = fr->nr[block];
}
ndo_real(fr->block[block],fr->nr[block],bOK1);
bOK = bOK && bOK1;
}
if(!bRead)
{
if( gmx_fio_flush(fp) != 0)
{
gmx_file("Cannot write energy file; maybe you are out of quota?");
}
}
if (!bOK)
{
if (bRead)
{
fprintf(stderr,"\nLast energy frame read %d",
framenr-1);
fprintf(stderr,"\nWARNING: Incomplete energy frame: nr %d time %8.3f\n",
framenr,fr->t);
}
else
{
gmx_fatal(FARGS,"could not write energies");
}
return FALSE;
}
return TRUE;
}
bool do_enx(int fp,t_enxframe *fr)
{
int i,block;
bool bRead,bOK,bOK1,bSane;
real tmp1,tmp2;
bOK = TRUE;
bRead = gmx_fio_getread(fp);
if (!bRead) {
fr->e_size = fr->nre*sizeof(fr->ener[0].e)*4;
fr->d_size = fr->ndisre*(sizeof(fr->disre_rm3tav[0]) +
sizeof(fr->disre_rt[0]));
}
gmx_fio_select(fp);
if (!do_eheader(fp,fr,&bOK)) {
if (bRead) {
fprintf(stderr,"\rLast energy frame read %d time %8.3f ",
framenr-1,frametime);
if (!bOK)
fprintf(stderr,
"\nWARNING: Incomplete energy frame: nr %d time %8.3f\n",
framenr,fr->t);
}
else
{
gmx_file("Cannot write energy file header; maybe you are out of quota?");
}
return FALSE;
}
if (bRead) {
if ((framenr < 20 || framenr % 10 == 0) &&
(framenr < 200 || framenr % 100 == 0) &&
(framenr < 2000 || framenr % 1000 == 0))
fprintf(stderr,"\rReading energy frame %6d time %8.3f ",
framenr,fr->t);
framenr++;
frametime = fr->t;
}
/* Check sanity of this header */
bSane = (fr->nre > 0 || fr->ndisre > 0);
for(block=0; block<fr->nblock; block++)
bSane = bSane || (fr->nr[block] > 0);
if (!((fr->step >= 0) && bSane)) {
fprintf(stderr,"\nWARNING: there may be something wrong with energy file %s\n",
gmx_fio_getname(fp));
fprintf(stderr,"Found: step=%d, nre=%d, ndisre=%d, nblock=%d, time=%g.\n"
"Trying to skip frame expect a crash though\n",
fr->step,fr->nre,fr->ndisre,fr->nblock,fr->t);
}
if (bRead && fr->nre>fr->e_alloc) {
srenew(fr->ener,fr->nre);
for(i=fr->e_alloc; (i<fr->nre); i++) {
fr->ener[i].e = fr->ener[i].eav =
fr->ener[i].esum = fr->ener[i].e2sum = 0;
}
fr->e_alloc = fr->nre;
}
for(i=0; i<fr->nre; i++) {
bOK = bOK && do_real(fr->ener[i].e);
tmp1 = fr->ener[i].eav;
bOK = bOK && do_real(tmp1);
if (bRead)
fr->ener[i].eav = tmp1;
/* This is to save only in single precision (unless compiled in DP) */
tmp2 = fr->ener[i].esum;
bOK = bOK && do_real(tmp2);
if (bRead)
fr->ener[i].esum = tmp2;
bOK = bOK && do_real(fr->ener[i].e2sum);
}
if (fr->ndisre) {
if (bRead && fr->ndisre>fr->d_alloc) {
srenew(fr->disre_rm3tav,fr->ndisre);
srenew(fr->disre_rt,fr->ndisre);
fr->d_alloc = fr->ndisre;
}
ndo_real(fr->disre_rm3tav,fr->ndisre,bOK1);
bOK = bOK && bOK1;
ndo_real(fr->disre_rt,fr->ndisre,bOK1);
bOK = bOK && bOK1;
}
for(block=0; block<fr->nblock; block++) {
if (bRead && fr->nr[block]>fr->b_alloc[block]) {
srenew(fr->block[block],fr->nr[block]);
fr->b_alloc[block] = fr->nr[block];
}
ndo_real(fr->block[block],fr->nr[block],bOK1);
bOK = bOK && bOK1;
}
if(!bRead)
{
if( gmx_fio_flush(fp) != 0)
{
gmx_file("Cannot write energy file; maybe you are out of quota?");
}
}
if (!bOK) {
if (bRead) {
fprintf(stderr,"\nLast energy frame read %d",
framenr-1);
fprintf(stderr,"\nWARNING: Incomplete energy frame: nr %d time %8.3f\n",
framenr,fr->t);
} else
gmx_fatal(FARGS,"could not write energies");
return FALSE;
}
return TRUE;
}