static void edr_nms(int fp,int *nre,char ***nms)
{
XDR *xdr;
bool bRead = gmx_fio_getread(fp);
int i;
char **NM;
xdr = gmx_fio_getxdr(fp);
NM=*nms;
if (!xdr_int(xdr,nre)) {
if(!bRead)
gmx_file("Cannot write energy names to file; maybe you are out of quota?");
*nre=0;
return;
}
if (*nre == -55555) {
/* In the 4.1 edr format the first entry is the magic number */
gmx_fatal(FARGS,"You are trying to read an edr file of GROMACS version 4.1 or later with GROMACS version 4.0");
}
if (NM == NULL) {
snew(NM,*nre);
}
for(i=0; i<*nre; i++) {
if (bRead && NM[i]) {
sfree(NM[i]);
NM[i] = NULL;
}
if(!xdr_string(xdr,&(NM[i]),STRLEN))
gmx_file("Cannot write energy names to file; maybe you are out of quota?");
}
*nms=NM;
}
static void edr_nms(int fp,int *nre,char ***nms)
{
XDR *xdr;
bool bRead = gmx_fio_getread(fp);
int i;
char **NM;
xdr = gmx_fio_getxdr(fp);
NM=*nms;
if (!xdr_int(xdr,nre)) {
*nre=0;
return;
}
if (NM == NULL) {
snew(NM,*nre);
}
for(i=0; i<*nre; i++) {
if (bRead && NM[i]) {
sfree(NM[i]);
NM[i] = NULL;
}
xdr_string(xdr,&(NM[i]),STRLEN);
}
*nms=NM;
}
static bool do_eheader(int fp,t_enxframe *fr,bool *bOK)
{
int block,i,dum=0;
bool bRead = gmx_fio_getread(fp);
int tempfix_nr=0;
*bOK=TRUE;
if (!do_real(fr->t))
{
return FALSE;
}
if (!do_int (fr->step) ||
!do_int (fr->nre) ||
!do_int (fr->ndisre) ||
!do_int (fr->nblock))
{
*bOK = FALSE;
}
if (*bOK && bRead && fr->nblock>70)
{
/* Temporary fix for intermediate file version, only used by B. Hess */
tempfix_nr = fr->nblock;
fr->nblock = 1;
}
if (*bOK && bRead && fr->nblock>fr->nr_alloc)
{
srenew(fr->nr,fr->nblock);
srenew(fr->b_alloc,fr->nblock);
srenew(fr->block,fr->nblock);
for(i=fr->nr_alloc; i<fr->nblock; i++) {
fr->block[i] = NULL;
fr->b_alloc[i] = 0;
}
fr->nr_alloc = fr->nblock;
}
if (tempfix_nr)
fr->nr[0] = tempfix_nr;
else
{
for(block=0; block<fr->nblock && *bOK; block++)
if (!do_int (fr->nr[block]))
*bOK = FALSE;
}
if(*bOK)
{
if (!do_int (fr->e_size) ||
!do_int (fr->d_size) ||
!do_int (dum))
{
*bOK = FALSE;
}
}
return *bOK;
}
void do_enxnms(ener_file_t ef,int *nre,gmx_enxnm_t **nms)
{
int magic=-55555;
XDR *xdr;
gmx_bool bRead = gmx_fio_getread(ef->fio);
int file_version;
int i;
gmx_fio_checktype(ef->fio);
xdr = gmx_fio_getxdr(ef->fio);
if (!xdr_int(xdr,&magic))
{
if(!bRead)
{
gmx_file("Cannot write energy names to file; maybe you are out of quota?");
}
*nre=0;
return;
}
if (magic > 0)
{
/* Assume this is an old edr format */
file_version = 1;
*nre = magic;
ef->eo.bOldFileOpen = TRUE;
ef->eo.bReadFirstStep = FALSE;
srenew(ef->eo.ener_prev,*nre);
}
else
{
ef->eo.bOldFileOpen=FALSE;
if (magic != -55555)
{
gmx_fatal(FARGS,"Energy names magic number mismatch, this is not a GROMACS edr file");
}
file_version = enx_version;
xdr_int(xdr,&file_version);
if (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);
}
xdr_int(xdr,nre);
}
if (file_version != enx_version)
{
fprintf(stderr,"Note: enx file_version %d, software version %d\n",
file_version,enx_version);
}
edr_strings(xdr,bRead,file_version,*nre,nms);
}
void do_enxnms(int fp,int *nre,char ***nms)
{
bool bRead;
bRead = gmx_fio_getread(fp);
if (gmx_fio_getftp(fp) == efEDR) {
gmx_fio_select(fp);
edr_nms(fp,nre,nms);
}
else if (bRead)
rd_ener_nms(gmx_fio_getfp(fp),nre,nms);
else
wr_ener_nms(gmx_fio_getfp(fp),*nre,*nms);
}
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->rav[0]) +
sizeof(fr->rt[0]));
}
gmx_fio_select(fp);
if (!do_eheader(fp,fr,&bOK)) {
if (bRead) {
fprintf(stderr,"\rLast frame read %d ",framenr-1);
if (!bOK)
fprintf(stderr,"\nWARNING: Incomplete frame: nr %6d time %8.3f\n",
framenr,fr->t);
}
return FALSE;
}
if (bRead) {
if ( ( framenr<10 ) || ( framenr%10 == 0) )
fprintf(stderr,"\rReading frame %6d time %8.3f ",framenr,fr->t);
framenr++;
}
/* 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);
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;
if((tmp1/(fr->step+1))<GMX_REAL_EPS)
tmp1=0;
bOK = bOK && do_real(tmp1);
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);
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->rav,fr->ndisre);
srenew(fr->rt,fr->ndisre);
fr->d_alloc = fr->ndisre;
}
ndo_real(fr->rav,fr->ndisre,bOK1);
bOK = bOK && bOK1;
ndo_real(fr->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 (!bOK) {
if (bRead) {
fprintf(stderr,"\nLast frame read %d ",
framenr-1);
fprintf(stderr,"\nWARNING: Incomplete frame: nr %6d time %8.3f \n",
framenr,fr->t);
} else
fatal_error(-1,"could not write energies");
return FALSE;
}
return TRUE;
}
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;
}
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;
}
static bool do_eheader(int fp,int *file_version,t_enxframe *fr,bool bTest,
bool *bOK)
{
int magic=-7777777;
real r;
int block,i,zero=0,dum=0;
bool bRead = gmx_fio_getread(fp);
int tempfix_nr=0;
*bOK=TRUE;
/* The original energy frame started with a real,
* so we have to use a real for compatibility.
*/
r = -2e10;
if (!do_real(r)) return FALSE;
if (r > -1e10)
{
/* Assume we are reading an old format */
*file_version = 1;
fr->t = r;
if (!do_int(dum)) *bOK = FALSE;
fr->step = dum;
}
else
{
if (!do_int (magic)) *bOK = FALSE;
if (magic != -7777777)
{
gmx_fatal(FARGS,"Energy header magic number mismatch, this is not a GROMACS edr file");
}
*file_version = enx_version;
if (!do_int (*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(fp),file_version,enx_version);
}
if (!do_double(fr->t)) *bOK = FALSE;
if (!do_gmx_step_t(fr->step)) *bOK = FALSE;
if (!bRead && fr->nsum == 1) {
/* Do not store sums of length 1,
* since this does not add information.
*/
if (!do_int (zero)) *bOK = FALSE;
} else {
if (!do_int (fr->nsum)) *bOK = FALSE;
}
if (*file_version >= 3)
{
do_gmx_step_t(fr->nsteps);
}
else
{
fr->nsteps = max(1,fr->nsum);
}
}
if (!do_int (fr->nre)) *bOK = FALSE;
if (!do_int (fr->ndisre)) *bOK = FALSE;
if (!do_int (fr->nblock)) *bOK = FALSE;
if (*bOK && bRead && fr->nblock>fr->nr_alloc)
{
srenew(fr->nr,fr->nblock);
srenew(fr->b_alloc,fr->nblock);
srenew(fr->block,fr->nblock);
for(i=fr->nr_alloc; i<fr->nblock; i++) {
fr->block[i] = NULL;
fr->b_alloc[i] = 0;
}
fr->nr_alloc = fr->nblock;
}
for(block=0; block<fr->nblock; block++)
{
if (!do_int (fr->nr[block]))
{
*bOK = FALSE;
}
}
if (!do_int (fr->e_size)) *bOK = FALSE;
if (!do_int (fr->d_size)) *bOK = FALSE;
/* Do a dummy int to keep the format compatible with the old code */
if (!do_int (dum)) *bOK = FALSE;
if (*bOK && *file_version == 1 && !bTest)
{
if (fp >= ener_old_nalloc)
{
gmx_incons("Problem with reading old format energy files");
}
if (!ener_old[fp].bReadFirstStep)
{
ener_old[fp].bReadFirstStep = TRUE;
ener_old[fp].first_step = fr->step;
ener_old[fp].nsum_prev = 0;
}
fr->nsum = fr->step - ener_old[fp].first_step + 1;
fr->nsteps = fr->nsum;
}
return *bOK;
}
void do_enxnms(int fp,int *nre,gmx_enxnm_t **nms)
{
int magic=-55555;
XDR *xdr;
bool bRead = gmx_fio_getread(fp);
int file_version;
int i;
gmx_fio_select(fp);
xdr = gmx_fio_getxdr(fp);
if (!xdr_int(xdr,&magic))
{
if(!bRead)
{
gmx_file("Cannot write energy names to file; maybe you are out of quota?");
}
*nre=0;
return;
}
if (magic > 0)
{
/* Assume this is an old edr format */
file_version = 1;
*nre = magic;
if (fp >= ener_old_nalloc)
{
srenew(ener_old,fp + 1);
for(i=ener_old_nalloc; i<fp+1; i++) {
ener_old[i].bOldFileOpen = FALSE;
ener_old[i].ener_prev = NULL;
}
ener_old_nalloc = fp + 1;
}
ener_old[fp].bOldFileOpen = TRUE;
ener_old[fp].bReadFirstStep = FALSE;
srenew(ener_old[fp].ener_prev,*nre);
}
else
{
if (fp < ener_old_nalloc)
{
ener_old[fp].bOldFileOpen = FALSE;
}
if (magic != -55555)
{
gmx_fatal(FARGS,"Energy names magic number mismatch, this is not a GROMACS edr file");
}
file_version = enx_version;
xdr_int(xdr,&file_version);
if (file_version > enx_version)
{
gmx_fatal(FARGS,"reading tpx file (%s) version %d with version %d program",gmx_fio_getname(fp),file_version,enx_version);
}
xdr_int(xdr,nre);
}
if (file_version != enx_version)
{
fprintf(stderr,"Note: enx file_version %d, software version %d\n",
file_version,enx_version);
}
edr_strings(xdr,bRead,file_version,*nre,nms);
}