static gmx_bool do_trnheader(t_fileio *fio, gmx_bool bRead, t_trnheader *sh, gmx_bool *bOK)
{
int magic = GROMACS_MAGIC;
static gmx_bool bFirst = TRUE;
char buf[256];
*bOK = TRUE;
gmx_fio_checktype(fio);
if (!gmx_fio_do_int(fio, magic) || magic != GROMACS_MAGIC)
{
return FALSE;
}
if (bRead)
{
*bOK = *bOK && gmx_fio_do_string(fio, buf);
if (bFirst)
{
fprintf(stderr, "trn version: %s ", buf);
}
}
else
{
sprintf(buf, "GMX_trn_file");
*bOK = *bOK && gmx_fio_do_string(fio, buf);
}
*bOK = *bOK && gmx_fio_do_int(fio, sh->ir_size);
*bOK = *bOK && gmx_fio_do_int(fio, sh->e_size);
*bOK = *bOK && gmx_fio_do_int(fio, sh->box_size);
*bOK = *bOK && gmx_fio_do_int(fio, sh->vir_size);
*bOK = *bOK && gmx_fio_do_int(fio, sh->pres_size);
*bOK = *bOK && gmx_fio_do_int(fio, sh->top_size);
*bOK = *bOK && gmx_fio_do_int(fio, sh->sym_size);
*bOK = *bOK && gmx_fio_do_int(fio, sh->x_size);
*bOK = *bOK && gmx_fio_do_int(fio, sh->v_size);
*bOK = *bOK && gmx_fio_do_int(fio, sh->f_size);
*bOK = *bOK && gmx_fio_do_int(fio, sh->natoms);
if (!*bOK)
{
return *bOK;
}
sh->bDouble = (nFloatSize(sh) == sizeof(double));
gmx_fio_setprecision(fio, sh->bDouble);
if (bRead && bFirst)
{
fprintf(stderr, "(%s precision)\n", sh->bDouble ? "double" : "single");
bFirst = FALSE;
}
*bOK = *bOK && gmx_fio_do_int(fio, sh->step);
*bOK = *bOK && gmx_fio_do_int(fio, sh->nre);
*bOK = *bOK && gmx_fio_do_real(fio, sh->t);
*bOK = *bOK && gmx_fio_do_real(fio, sh->lambda);
return *bOK;
}
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;
}
static gmx_bool do_eheader(ener_file_t ef,int *file_version,t_enxframe *fr,
int nre_test,gmx_bool *bWrongPrecision,gmx_bool *bOK)
{
int magic=-7777777;
real first_real_to_check;
int b,i,zero=0,dum=0;
gmx_bool bRead = gmx_fio_getread(ef->fio);
int tempfix_nr=0;
int ndisre=0;
int startb=0;
#ifndef GMX_DOUBLE
xdr_datatype dtreal=xdr_datatype_float;
#else
xdr_datatype dtreal=xdr_datatype_double;
#endif
if (nre_test >= 0)
{
*bWrongPrecision = FALSE;
}
*bOK=TRUE;
/* The original energy frame started with a real,
* so we have to use a real for compatibility.
* This is VERY DIRTY code, since do_eheader can be called
* with the wrong precision set and then we could read r > -1e10,
* while actually the intention was r < -1e10.
* When nre_test >= 0, do_eheader should therefore terminate
* before the number of i/o calls starts depending on what has been read
* (which is the case for for instance the block sizes for variable
* number of blocks, where this number is read before).
*/
first_real_to_check = -2e10;
if (!gmx_fio_do_real(ef->fio, first_real_to_check))
{
return FALSE;
}
if (first_real_to_check > -1e10)
{
/* Assume we are reading an old format */
*file_version = 1;
fr->t = first_real_to_check;
if (!gmx_fio_do_int(ef->fio, dum)) *bOK = FALSE;
fr->step = dum;
}
else
{
if (!gmx_fio_do_int(ef->fio, magic)) *bOK = FALSE;
if (magic != -7777777)
{
enx_warning("Energy header magic number mismatch, this is not a GROMACS edr file");
*bOK=FALSE;
return FALSE;
}
*file_version = enx_version;
if (!gmx_fio_do_int(ef->fio, *file_version)) *bOK = FALSE;
if (*bOK && *file_version > enx_version)
{
gmx_fatal(FARGS,"reading tpx file (%s) version %d with version %d program",gmx_fio_getname(ef->fio),file_version,enx_version);
}
if (!gmx_fio_do_double(ef->fio, fr->t)) *bOK = FALSE;
if (!gmx_fio_do_gmx_large_int(ef->fio, fr->step)) *bOK = FALSE;
if (!bRead && fr->nsum == 1) {
/* Do not store sums of length 1,
* since this does not add information.
*/
if (!gmx_fio_do_int(ef->fio, zero)) *bOK = FALSE;
} else {
if (!gmx_fio_do_int(ef->fio, fr->nsum)) *bOK = FALSE;
}
if (*file_version >= 3)
{
if (!gmx_fio_do_gmx_large_int(ef->fio, fr->nsteps)) *bOK = FALSE;
}
else
{
fr->nsteps = max(1,fr->nsum);
}
if (*file_version >= 5)
{
if (!gmx_fio_do_double(ef->fio, fr->dt)) *bOK = FALSE;
}
else
{
fr->dt = 0;
}
}
if (!gmx_fio_do_int(ef->fio, fr->nre)) *bOK = FALSE;
if (*file_version < 4)
{
if (!gmx_fio_do_int(ef->fio, ndisre)) *bOK = FALSE;
}
else
{
/* now reserved for possible future use */
if (!gmx_fio_do_int(ef->fio, dum)) *bOK = FALSE;
}
if (!gmx_fio_do_int(ef->fio, fr->nblock)) *bOK = FALSE;
if (fr->nblock < 0) *bOK=FALSE;
if (ndisre!=0)
{
if (*file_version >= 4)
{
enx_warning("Distance restraint blocks in old style in new style file");
*bOK=FALSE;
return FALSE;
}
fr->nblock+=1;
}
/* Frames could have nre=0, so we can not rely only on the fr->nre check */
if (bRead && nre_test >= 0 &&
((fr->nre > 0 && fr->nre != nre_test) ||
fr->nre < 0 || ndisre < 0 || fr->nblock < 0))
{
*bWrongPrecision = TRUE;
return *bOK;
}
/* we now know what these should be, or we've already bailed out because
of wrong precision */
if ( *file_version==1 && (fr->t < 0 || fr->t > 1e20 || fr->step < 0 ) )
{
enx_warning("edr file with negative step number or unreasonable time (and without version number).");
*bOK=FALSE;
return FALSE;
}
if (*bOK && bRead)
{
add_blocks_enxframe(fr, fr->nblock);
}
startb=0;
if (ndisre>0)
{
/* sub[0] is the instantaneous data, sub[1] is time averaged */
add_subblocks_enxblock(&(fr->block[0]), 2);
fr->block[0].id=enxDISRE;
fr->block[0].sub[0].nr=ndisre;
fr->block[0].sub[1].nr=ndisre;
fr->block[0].sub[0].type=dtreal;
fr->block[0].sub[1].type=dtreal;
startb++;
}
/* read block header info */
for(b=startb; b<fr->nblock; b++)
{
if (*file_version<4)
{
/* blocks in old version files always have 1 subblock that
consists of reals. */
int nrint;
if (bRead)
{
add_subblocks_enxblock(&(fr->block[b]), 1);
}
else
{
if (fr->block[b].nsub != 1)
{
gmx_incons("Writing an old version .edr file with too many subblocks");
}
if (fr->block[b].sub[0].type != dtreal)
{
gmx_incons("Writing an old version .edr file the wrong subblock type");
}
}
nrint = fr->block[b].sub[0].nr;
if (!gmx_fio_do_int(ef->fio, nrint))
{
*bOK = FALSE;
}
fr->block[b].id = b - startb;
fr->block[b].sub[0].nr = nrint;
fr->block[b].sub[0].type = dtreal;
}
else
{
int i;
/* in the new version files, the block header only contains
the ID and the number of subblocks */
int nsub=fr->block[b].nsub;
*bOK = *bOK && gmx_fio_do_int(ef->fio, fr->block[b].id);
*bOK = *bOK && gmx_fio_do_int(ef->fio, nsub);
fr->block[b].nsub=nsub;
if (bRead)
add_subblocks_enxblock(&(fr->block[b]), nsub);
/* read/write type & size for each subblock */
for(i=0;i<nsub;i++)
{
t_enxsubblock *sub=&(fr->block[b].sub[i]); /* shortcut */
int typenr=sub->type;
*bOK=*bOK && gmx_fio_do_int(ef->fio, typenr);
*bOK=*bOK && gmx_fio_do_int(ef->fio, sub->nr);
sub->type = (xdr_datatype)typenr;
}
}
}
if (!gmx_fio_do_int(ef->fio, fr->e_size)) *bOK = FALSE;
/* now reserved for possible future use */
if (!gmx_fio_do_int(ef->fio, dum)) *bOK = FALSE;
/* Do a dummy int to keep the format compatible with the old code */
if (!gmx_fio_do_int(ef->fio, dum)) *bOK = FALSE;
if (*bOK && *file_version == 1 && nre_test < 0)
{
#if 0
if (fp >= ener_old_nalloc)
{
gmx_incons("Problem with reading old format energy files");
}
#endif
if (!ef->eo.bReadFirstStep)
{
ef->eo.bReadFirstStep = TRUE;
ef->eo.first_step = fr->step;
ef->eo.step_prev = fr->step;
ef->eo.nsum_prev = 0;
}
fr->nsum = fr->step - ef->eo.first_step + 1;
fr->nsteps = fr->step - ef->eo.step_prev;
fr->dt = 0;
}
return *bOK;
}
void gmx_mtxio_write(const char * filename,
int nrow,
int ncol,
real * full_matrix,
gmx_sparsematrix_t * sparse_matrix)
{
t_fileio *fio;
XDR * xd;
int i,j,prec;
gmx_bool bDum = TRUE;
gmx_bool bRead = FALSE;
size_t sz;
if(full_matrix!=NULL && sparse_matrix!=NULL)
{
gmx_fatal(FARGS,"Both full AND sparse matrix specified to gmx_mtxio_write().\n");
}
fio = gmx_fio_open(filename,"w");
gmx_fio_checktype(fio);
xd = gmx_fio_getxdr(fio);
/* Write magic number */
i = GMX_MTXIO_MAGIC_NUMBER;
gmx_fio_do_int(fio, i);
/* Write generating Gromacs version */
gmx_fio_write_string(fio, GromacsVersion());
/* Write 1 for double, 0 for single precision */
if(sizeof(real)==sizeof(double))
prec = 1;
else
prec = 0;
gmx_fio_do_int(fio, prec);
gmx_fio_do_int(fio, nrow);
gmx_fio_do_int(fio, ncol);
if(full_matrix!=NULL)
{
/* Full matrix storage format */
i = GMX_MTXIO_FULL_MATRIX;
gmx_fio_do_int(fio, i);
sz = nrow*ncol;
bDum=gmx_fio_ndo_real(fio, full_matrix,sz);
}
else
{
/* Sparse storage */
i = GMX_MTXIO_SPARSE_MATRIX;
gmx_fio_do_int(fio, i);
gmx_fio_do_gmx_bool(fio, sparse_matrix->compressed_symmetric);
gmx_fio_do_int(fio, sparse_matrix->nrow);
if(sparse_matrix->nrow != nrow)
{
gmx_fatal(FARGS,"Internal inconsistency in sparse matrix.\n");
}
bDum=gmx_fio_ndo_int(fio, sparse_matrix->ndata,sparse_matrix->nrow);
for(i=0;i<sparse_matrix->nrow;i++)
{
for(j=0;j<sparse_matrix->ndata[i];j++)
{
gmx_fio_do_int(fio, sparse_matrix->data[i][j].col);
gmx_fio_do_real(fio, sparse_matrix->data[i][j].value);
}
}
}
gmx_fio_close(fio);
}
void
gmx_mtxio_read (const char * filename,
int * nrow,
int * ncol,
real ** full_matrix,
gmx_sparsematrix_t ** sparse_matrix)
{
t_fileio *fio;
XDR * xd;
int i,j,prec;
gmx_bool bDum = TRUE;
gmx_bool bRead = TRUE;
char gmxver[256];
size_t sz;
fio = gmx_fio_open(filename,"r");
gmx_fio_checktype(fio);
xd = gmx_fio_getxdr(fio);
/* Read and check magic number */
i = GMX_MTXIO_MAGIC_NUMBER;
gmx_fio_do_int(fio, i);
if(i!=GMX_MTXIO_MAGIC_NUMBER)
{
gmx_fatal(FARGS,
"No matrix data found in file. Note that the Hessian matrix format changed\n"
"in Gromacs 3.3 to enable portable files and sparse matrix storage.\n");
}
/* Read generating Gromacs version */
gmx_fio_do_string(fio, gmxver);
/* Write 1 for double, 0 for single precision */
if(sizeof(real)==sizeof(double))
prec = 1;
else
prec = 0;
gmx_fio_do_int(fio, prec);
fprintf(stderr,"Reading %s precision matrix generated by Gromacs %s\n",
(prec == 1) ? "double" : "single",gmxver);
gmx_fio_do_int(fio, i);
*nrow=i;
gmx_fio_do_int(fio, i);
*ncol=i;
gmx_fio_do_int(fio, i);
if(i==GMX_MTXIO_FULL_MATRIX)
{
printf("Full matrix storage format, nrow=%d, ncols=%d\n",*nrow,*ncol);
sz = (*nrow) * (*ncol);
snew((*full_matrix),sz);
bDum=gmx_fio_ndo_real(fio, (*full_matrix),sz);
}
else
{
/* Sparse storage */
printf("Sparse matrix storage format, nrow=%d, ncols=%d\n",*nrow,*ncol);
snew((*sparse_matrix),1);
gmx_fio_do_gmx_bool(fio, (*sparse_matrix)->compressed_symmetric);
gmx_fio_do_int(fio, (*sparse_matrix)->nrow);
if((*sparse_matrix)->nrow != *nrow)
{
gmx_fatal(FARGS,"Internal inconsistency in sparse matrix.\n");
}
snew((*sparse_matrix)->ndata,(*sparse_matrix)->nrow);
snew((*sparse_matrix)->nalloc,(*sparse_matrix)->nrow);
snew((*sparse_matrix)->data,(*sparse_matrix)->nrow);
bDum=gmx_fio_ndo_int(fio, (*sparse_matrix)->ndata,
(*sparse_matrix)->nrow);
for(i=0;i<(*sparse_matrix)->nrow;i++)
{
(*sparse_matrix)->nalloc[i] = (*sparse_matrix)->ndata[i] + 10;
snew(((*sparse_matrix)->data[i]),(*sparse_matrix)->nalloc[i]);
for(j=0;j<(*sparse_matrix)->ndata[i];j++)
{
gmx_fio_do_int(fio, (*sparse_matrix)->data[i][j].col);
gmx_fio_do_real(fio, (*sparse_matrix)->data[i][j].value);
}
}
}
gmx_fio_close(fio);
}