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);
}
static bool do_trnheader(int fp,bool bRead,t_trnheader *sh, bool *bOK)
{
const int magic=GROMACS_MAGIC;
const char *version = "GMX_trn_file";
static bool bFirst=TRUE;
char buf[256];
*bOK=TRUE;
gmx_fio_select(fp);
if (!do_int(magic))
return FALSE;
if (bRead) {
*bOK = *bOK && do_string(buf);
if (bFirst)
fprintf(stderr,"trn version: %s ",buf);
}
else
*bOK = *bOK && do_string(version);
*bOK = *bOK && do_int(sh->ir_size);
*bOK = *bOK && do_int(sh->e_size);
*bOK = *bOK && do_int(sh->box_size);
*bOK = *bOK && do_int(sh->vir_size);
*bOK = *bOK && do_int(sh->pres_size);
*bOK = *bOK && do_int(sh->top_size);
*bOK = *bOK && do_int(sh->sym_size);
*bOK = *bOK && do_int(sh->x_size);
*bOK = *bOK && do_int(sh->v_size);
*bOK = *bOK && do_int(sh->f_size);
*bOK = *bOK && do_int(sh->natoms);
if (!*bOK) return *bOK;
sh->bDouble = (nFloatSize(sh) == sizeof(double));
gmx_fio_setprecision(fp,sh->bDouble);
if (bRead && bFirst) {
fprintf(stderr,"(%s precision)\n",sh->bDouble ? "double" : "single");
bFirst = FALSE;
}
*bOK = *bOK && do_int(sh->step);
*bOK = *bOK && do_int(sh->nre);
*bOK = *bOK && do_real(sh->t);
*bOK = *bOK && do_real(sh->lambda);
return *bOK;
}
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;
}
int open_enx(char *fn,char *mode)
{
int fp,nre,i;
char **nm=NULL;
t_enxframe *fr;
bool bDum=TRUE;
/* Energy files should always be opened as binary files,
* but that is checked in gmx_fio_open.
*/
if (mode[0]=='r') {
fp=gmx_fio_open(fn,mode);
gmx_fio_select(fp);
gmx_fio_setprecision(fp,FALSE);
do_enxnms(fp,&nre,&nm);
snew(fr,1);
do_eheader(fp,fr,&bDum);
/* Now check whether this file is in single precision */
if (((fr->e_size && (fr->nre == nre) &&
(nre*4*sizeof(float) == fr->e_size)) ||
(fr->d_size &&
(fr->ndisre*sizeof(float)*2+sizeof(int) == fr->d_size)))){
fprintf(stderr,"Opened %s as single precision energy file\n",fn);
for(i=0; (i<nre); i++)
sfree(nm[i]);
sfree(nm);
}
else {
gmx_fio_rewind(fp);
gmx_fio_select(fp);
gmx_fio_setprecision(fp,TRUE);
do_enxnms(fp,&nre,&nm);
do_eheader(fp,fr,&bDum);
if (((fr->e_size && (fr->nre == nre) &&
(nre*4*sizeof(double) == fr->e_size)) ||
(fr->d_size &&
(fr->ndisre*sizeof(double)*2+sizeof(int) == fr->d_size))))
fprintf(stderr,"Opened %s as double precision energy file\n",fn);
else {
if (empty_file(fn))
fatal_error(0,"File %s is empty",fn);
else
fatal_error(0,"Energy file %s not recognized, maybe different CPU?",
fn);
}
for(i=0; (i<nre); i++)
sfree(nm[i]);
sfree(nm);
}
free_enxframe(fr);
sfree(fr);
gmx_fio_rewind(fp);
}
else
fp = gmx_fio_open(fn,mode);
framenr=0;
return fp;
}
void
gmx_mtxio_write(char * filename,
int nrow,
int ncol,
real * full_matrix,
gmx_sparsematrix_t * sparse_matrix)
{
int fd;
XDR * xd;
int i,j,prec;
bool bDum = TRUE;
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");
}
fd = gmx_fio_open(filename,"w");
gmx_fio_select(fd);
xd = gmx_fio_getxdr(fd);
/* Write magic number */
i = GMX_MTXIO_MAGIC_NUMBER;
do_int(i);
/* Write generating Gromacs version */
do_string(GromacsVersion());
/* Write 1 for double, 0 for single precision */
if(sizeof(real)==sizeof(double))
prec = 1;
else
prec = 0;
do_int(prec);
do_int(nrow);
do_int(ncol);
if(full_matrix!=NULL)
{
/* Full matrix storage format */
i = GMX_MTXIO_FULL_MATRIX;
do_int(i);
sz = nrow*ncol;
ndo_real(full_matrix,sz,bDum);
}
else
{
/* Sparse storage */
i = GMX_MTXIO_SPARSE_MATRIX;
do_int(i);
do_int(sparse_matrix->compressed_symmetric);
do_int(sparse_matrix->nrow);
if(sparse_matrix->nrow != nrow)
{
gmx_fatal(FARGS,"Internal inconsistency in sparse matrix.\n");
}
ndo_int(sparse_matrix->ndata,sparse_matrix->nrow,bDum);
for(i=0; i<sparse_matrix->nrow; i++)
{
for(j=0; j<sparse_matrix->ndata[i]; j++)
{
do_int(sparse_matrix->data[i][j].col);
do_real(sparse_matrix->data[i][j].value);
}
}
}
gmx_fio_close(fd);
}
void
gmx_mtxio_read (char * filename,
int * nrow,
int * ncol,
real ** full_matrix,
gmx_sparsematrix_t ** sparse_matrix)
{
int fd;
XDR * xd;
int i,j,prec;
bool bDum = TRUE;
bool bRead = TRUE;
char gmxver[256];
size_t sz;
fd = gmx_fio_open(filename,"r");
gmx_fio_select(fd);
xd = gmx_fio_getxdr(fd);
/* Read and check magic number */
i = GMX_MTXIO_MAGIC_NUMBER;
do_int(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 */
do_string(gmxver);
/* Write 1 for double, 0 for single precision */
if(sizeof(real)==sizeof(double))
prec = 1;
else
prec = 0;
do_int(prec);
fprintf(stderr,"Reading %s precision matrix generated by Gromacs %s\n",
(prec == 1) ? "double" : "single",gmxver);
do_int(i);
*nrow=i;
do_int(i);
*ncol=i;
do_int(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);
ndo_real((*full_matrix),sz,bDum);
}
else
{
/* Sparse storage */
printf("Sparse matrix storage format, nrow=%d, ncols=%d\n",*nrow,*ncol);
snew((*sparse_matrix),1);
do_int((*sparse_matrix)->compressed_symmetric);
do_int((*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);
ndo_int((*sparse_matrix)->ndata,(*sparse_matrix)->nrow,bDum);
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++)
{
do_int((*sparse_matrix)->data[i][j].col);
do_real((*sparse_matrix)->data[i][j].value);
}
}
}
gmx_fio_close(fd);
}
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;
}
int open_enx(const char *fn,const char *mode)
{
int fp,nre,i;
gmx_enxnm_t *nms=NULL;
int file_version=-1;
t_enxframe *fr;
bool bDum=TRUE;
if (mode[0]=='r') {
fp=gmx_fio_open(fn,mode);
gmx_fio_select(fp);
gmx_fio_setprecision(fp,FALSE);
do_enxnms(fp,&nre,&nms);
snew(fr,1);
do_eheader(fp,&file_version,fr,TRUE,&bDum);
if(!bDum)
{
gmx_file("Cannot read energy file header. Corrupt file?");
}
/* Now check whether this file is in single precision */
if (((fr->e_size && (fr->nre == nre) &&
(nre*4*sizeof(float) == fr->e_size)) ||
(fr->d_size &&
(fr->ndisre*sizeof(float)*2+sizeof(int) == fr->d_size)))){
fprintf(stderr,"Opened %s as single precision energy file\n",fn);
free_enxnms(nre,nms);
}
else {
gmx_fio_rewind(fp);
gmx_fio_select(fp);
gmx_fio_setprecision(fp,TRUE);
do_enxnms(fp,&nre,&nms);
do_eheader(fp,&file_version,fr,TRUE,&bDum);
if(!bDum)
{
gmx_file("Cannot write energy file header; maybe you are out of quota?");
}
if (((fr->e_size && (fr->nre == nre) &&
(nre*4*sizeof(double) == fr->e_size)) ||
(fr->d_size &&
(fr->ndisre*sizeof(double)*2+sizeof(int) == fr->d_size))))
fprintf(stderr,"Opened %s as double precision energy file\n",fn);
else {
if (empty_file(fn))
gmx_fatal(FARGS,"File %s is empty",fn);
else
gmx_fatal(FARGS,"Energy file %s not recognized, maybe different CPU?",
fn);
}
free_enxnms(nre,nms);
}
free_enxframe(fr);
sfree(fr);
gmx_fio_rewind(fp);
}
else
fp = gmx_fio_open(fn,mode);
framenr=0;
frametime=0;
return fp;
}
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);
}
