void close_enx(int fp)
{
if(gmx_fio_close(fp) != 0)
{
gmx_file("Cannot close energy file; it might be corrupt, or maybe you are out of quota?");
}
}
void close_enx(ener_file_t ef)
{
if(gmx_fio_close(ef->fio) != 0)
{
gmx_file("Cannot close energy file; it might be corrupt, or maybe you are out of quota?");
}
}
void close_trj(t_trxstatus *status)
{
gmx_fio_close(status->fio);
/* The memory in status->xframe is lost here,
* but the read_first_x/read_next_x functions are deprecated anyhow.
* read_first_frame/read_next_frame and close_trx should be used.
*/
sfree(status);
}
void close_trx(t_trxstatus *status)
{
gmx_tng_close(&status->tng);
if (status->fio)
{
gmx_fio_close(status->fio);
}
sfree(status);
}
void close_enx(ener_file_t ef)
{
if (ef == NULL)
{
// Nothing to do
return;
}
if (gmx_fio_close(ef->fio) != 0)
{
gmx_file("Cannot close energy file; it might be corrupt, or maybe you are out of disk space?");
}
}
void close_trx(t_trxstatus *status)
{
if (status == nullptr)
{
return;
}
gmx_tng_close(&status->tng);
if (status->fio)
{
gmx_fio_close(status->fio);
}
sfree(status);
}
void close_trj(t_trxstatus *status)
{
if (status == nullptr)
{
return;
}
gmx_tng_close(&status->tng);
if (status->fio)
{
gmx_fio_close(status->fio);
}
/* The memory in status->xframe is lost here,
* but the read_first_x/read_next_x functions are deprecated anyhow.
* read_first_frame/read_next_frame and close_trx should be used.
*/
sfree(status);
}
int
gmx_fio_fclose(FILE *fp)
{
int i,rc,found;
found = 0;
rc = -1;
for(i=0; i<nFIO && !found; i++)
{
if(fp == FIO[i].fp)
{
rc = gmx_fio_close(i);
found=1;
}
}
return rc;
}
void close_trx(t_trxstatus *status)
{
if (status == nullptr)
{
return;
}
gmx_tng_close(&status->tng);
if (status->fio)
{
gmx_fio_close(status->fio);
}
sfree(status->persistent_line);
#if GMX_USE_PLUGINS
sfree(status->vmdplugin);
#endif
/* The memory in status->xframe is lost here,
* but the read_first_x/read_next_x functions are deprecated anyhow.
* read_first_frame/read_next_frame and close_trx should be used.
*/
sfree(status);
}
void close_xtc(t_fileio *fio)
{
gmx_fio_close(fio);
}
int read_first_frame(const output_env_t oenv,t_trxstatus **status,
const char *fn,t_trxframe *fr,int flags)
{
t_fileio *fio;
gmx_bool bFirst,bOK;
int dummy=0;
clear_trxframe(fr,TRUE);
fr->flags = flags;
bFirst = TRUE;
snew((*status), 1);
status_init( *status );
(*status)->nxframe=1;
initcount(*status);
fio = (*status)->fio =gmx_fio_open(fn,"r");
switch (gmx_fio_getftp(fio))
{
case efTRJ:
case efTRR:
break;
case efCPT:
read_checkpoint_trxframe(fio,fr);
bFirst = FALSE;
break;
case efG96:
/* Can not rewind a compressed file, so open it twice */
read_g96_conf(gmx_fio_getfp(fio),fn,fr);
gmx_fio_close(fio);
clear_trxframe(fr,FALSE);
if (flags & (TRX_READ_X | TRX_NEED_X))
snew(fr->x,fr->natoms);
if (flags & (TRX_READ_V | TRX_NEED_V))
snew(fr->v,fr->natoms);
fio = (*status)->fio =gmx_fio_open(fn,"r");
break;
case efG87:
fr->natoms=xyz_first_x(*status, gmx_fio_getfp(fio),oenv,&fr->time,
&fr->x,fr->box);
if (fr->natoms) {
fr->bTime = TRUE;
fr->bX = TRUE;
fr->bBox = TRUE;
printcount(*status,oenv,fr->time,FALSE);
}
bFirst = FALSE;
break;
case efXTC:
if (read_first_xtc(fio,&fr->natoms,&fr->step,&fr->time,fr->box,&fr->x,
&fr->prec,&bOK) == 0) {
if (bOK) {
gmx_fatal(FARGS,"No XTC!\n");
} else {
fr->not_ok = DATA_NOT_OK;
}
}
if (fr->not_ok) {
fr->natoms = 0;
printincomp(*status,fr);
} else {
fr->bPrec = (fr->prec > 0);
fr->bStep = TRUE;
fr->bTime = TRUE;
fr->bX = TRUE;
fr->bBox = TRUE;
printcount(*status,oenv,fr->time,FALSE);
}
bFirst = FALSE;
break;
case efPDB:
pdb_first_x(*status, gmx_fio_getfp(fio),fr);
if (fr->natoms)
printcount(*status,oenv,fr->time,FALSE);
bFirst = FALSE;
break;
case efGRO:
if (gro_first_x_or_v(gmx_fio_getfp(fio),fr))
printcount(*status,oenv,fr->time,FALSE);
bFirst = FALSE;
break;
default:
#ifdef GMX_DLOPEN
gmx_fio_fp_close(fio); /*only close the file without removing FIO entry*/
if (!read_first_vmd_frame(&dummy,fn,fr,flags))
{
gmx_fatal(FARGS,"Not supported in read_first_frame: %s",fn);
}
#else
gmx_fatal(FARGS,"Not supported in read_first_frame: %s",fn);
#endif
break;
}
/* Return FALSE if we read a frame that's past the set ending time. */
if (!bFirst && (!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) > 0)) {
fr->t0 = fr->time;
return FALSE;
}
if (bFirst ||
(!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) < 0))
/* Read a frame when no frame was read or the first was skipped */
if (!read_next_frame(oenv,*status,fr))
return FALSE;
fr->t0 = fr->time;
return (fr->natoms > 0);
}
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);
}
void close_trn(int fp)
{
gmx_fio_close(fp);
}
void close_enx(int fp)
{
gmx_fio_close(fp);
}
void gmx_trr_close(t_fileio *fio)
{
gmx_fio_close(fio);
}
void gmx_mtxio_write(const char * filename,
int nrow,
int ncol,
real * full_matrix,
gmx_sparsematrix_t * sparse_matrix)
{
t_fileio *fio;
int i, j, prec;
size_t sz;
if (full_matrix != nullptr && sparse_matrix != nullptr)
{
gmx_fatal(FARGS, "Both full AND sparse matrix specified to gmx_mtxio_write().\n");
}
fio = gmx_fio_open(filename, "w");
/* Write magic number */
i = GMX_MTXIO_MAGIC_NUMBER;
gmx_fio_do_int(fio, i);
/* Write generating Gromacs version */
gmx_fio_write_string(fio, gmx_version());
/* 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 != nullptr)
{
/* Full matrix storage format */
i = GMX_MTXIO_FULL_MATRIX;
gmx_fio_do_int(fio, i);
sz = nrow*ncol;
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");
}
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 close_trn(t_fileio *fio)
{
gmx_fio_close(fio);
}
void close_trx(t_trxstatus *status)
{
gmx_fio_close(status->fio);
sfree(status);
}
int read_first_frame(const output_env_t oenv, t_trxstatus **status,
const char *fn, t_trxframe *fr, int flags)
{
t_fileio *fio;
gmx_bool bFirst, bOK;
int dummy = 0;
clear_trxframe(fr, TRUE);
fr->flags = flags;
bFirst = TRUE;
snew((*status), 1);
status_init( *status );
(*status)->nxframe = 1;
initcount(*status);
fio = (*status)->fio = gmx_fio_open(fn, "r");
switch (gmx_fio_getftp(fio))
{
case efTRJ:
case efTRR:
break;
case efCPT:
read_checkpoint_trxframe(fio, fr);
bFirst = FALSE;
break;
case efG96:
/* Can not rewind a compressed file, so open it twice */
if (!(*status)->persistent_line)
{
/* allocate the persistent line */
snew((*status)->persistent_line, STRLEN+1);
}
read_g96_conf(gmx_fio_getfp(fio), fn, fr, (*status)->persistent_line);
gmx_fio_close(fio);
clear_trxframe(fr, FALSE);
if (flags & (TRX_READ_X | TRX_NEED_X))
{
snew(fr->x, fr->natoms);
}
if (flags & (TRX_READ_V | TRX_NEED_V))
{
snew(fr->v, fr->natoms);
}
fio = (*status)->fio = gmx_fio_open(fn, "r");
break;
case efG87:
fr->natoms = xyz_first_x(*status, gmx_fio_getfp(fio), oenv, &fr->time,
&fr->x, fr->box);
if (fr->natoms)
{
fr->bTime = TRUE;
fr->bX = TRUE;
fr->bBox = TRUE;
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
case efXTC:
if (read_first_xtc(fio, &fr->natoms, &fr->step, &fr->time, fr->box, &fr->x,
&fr->prec, &bOK) == 0)
{
if (bOK)
{
gmx_fatal(FARGS, "No XTC!\n");
}
else
{
fr->not_ok = DATA_NOT_OK;
}
}
if (fr->not_ok)
{
fr->natoms = 0;
printincomp(*status, fr);
}
else
{
fr->bPrec = (fr->prec > 0);
fr->bStep = TRUE;
fr->bTime = TRUE;
fr->bX = TRUE;
fr->bBox = TRUE;
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
case efPDB:
pdb_first_x(*status, gmx_fio_getfp(fio), fr);
if (fr->natoms)
{
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
case efGRO:
if (gro_first_x_or_v(gmx_fio_getfp(fio), fr))
{
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
default:
#ifdef GMX_USE_PLUGINS
fprintf(stderr, "The file format of %s is not a known trajectory format to GROMACS.\n"
"Please make sure that the file is a trajectory!\n"
"GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins.\n"
"This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD.\n", fn);
gmx_fio_fp_close(fio); /*only close the file without removing FIO entry*/
if (!read_first_vmd_frame(fn, fr))
{
gmx_fatal(FARGS, "Not supported in read_first_frame: %s", fn);
}
#else
gmx_fatal(FARGS, "Not supported in read_first_frame: %s. Please make sure that the file is a trajectory.\n"
"GROMACS is not compiled with plug-in support. Thus it cannot read non-GROMACS trajectory formats using the VMD plug-ins.\n"
"Please compile with plug-in support if you want to read non-GROMACS trajectory formats.\n", fn);
#endif
break;
}
/* Return FALSE if we read a frame that's past the set ending time. */
if (!bFirst && (!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) > 0))
{
fr->t0 = fr->time;
return FALSE;
}
if (bFirst ||
(!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) < 0))
{
/* Read a frame when no frame was read or the first was skipped */
if (!read_next_frame(oenv, *status, fr))
{
return FALSE;
}
}
fr->t0 = fr->time;
return (fr->natoms > 0);
}
bool read_first_frame(const gmx_output_env_t *oenv, t_trxstatus **status,
const char *fn, t_trxframe *fr, int flags)
{
t_fileio *fio = nullptr;
gmx_bool bFirst, bOK;
int ftp = fn2ftp(fn);
clear_trxframe(fr, TRUE);
bFirst = TRUE;
snew((*status), 1);
status_init( *status );
initcount(*status);
(*status)->flags = flags;
if (efTNG == ftp)
{
/* Special treatment for TNG files */
gmx_tng_open(fn, 'r', &(*status)->tng);
}
else
{
fio = (*status)->fio = gmx_fio_open(fn, "r");
}
switch (ftp)
{
case efTRR:
break;
case efCPT:
read_checkpoint_trxframe(fio, fr);
bFirst = FALSE;
break;
case efG96:
{
/* Can not rewind a compressed file, so open it twice */
if (!(*status)->persistent_line)
{
/* allocate the persistent line */
snew((*status)->persistent_line, STRLEN+1);
}
t_symtab *symtab = nullptr;
read_g96_conf(gmx_fio_getfp(fio), fn, nullptr, fr, symtab, (*status)->persistent_line);
gmx_fio_close(fio);
clear_trxframe(fr, FALSE);
if (flags & (TRX_READ_X | TRX_NEED_X))
{
snew(fr->x, fr->natoms);
}
if (flags & (TRX_READ_V | TRX_NEED_V))
{
snew(fr->v, fr->natoms);
}
(*status)->fio = gmx_fio_open(fn, "r");
break;
}
case efXTC:
if (read_first_xtc(fio, &fr->natoms, &fr->step, &fr->time, fr->box, &fr->x,
&fr->prec, &bOK) == 0)
{
GMX_RELEASE_ASSERT(!bOK, "Inconsistent results - OK status from read_first_xtc, but 0 atom coords read");
fr->not_ok = DATA_NOT_OK;
}
if (fr->not_ok)
{
fr->natoms = 0;
printincomp(*status, fr);
}
else
{
fr->bPrec = (fr->prec > 0);
fr->bStep = TRUE;
fr->bTime = TRUE;
fr->bX = TRUE;
fr->bBox = TRUE;
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
case efTNG:
fr->step = -1;
if (!gmx_read_next_tng_frame((*status)->tng, fr, nullptr, 0))
{
fr->not_ok = DATA_NOT_OK;
fr->natoms = 0;
printincomp(*status, fr);
}
else
{
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
case efPDB:
pdb_first_x(*status, gmx_fio_getfp(fio), fr);
if (fr->natoms)
{
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
case efGRO:
if (gro_first_x_or_v(gmx_fio_getfp(fio), fr))
{
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
default:
#if GMX_USE_PLUGINS
fprintf(stderr, "The file format of %s is not a known trajectory format to GROMACS.\n"
"Please make sure that the file is a trajectory!\n"
"GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins.\n"
"This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD.\n", fn);
gmx_fio_fp_close(fio); /*only close the file without removing FIO entry*/
if (!read_first_vmd_frame(fn, &(*status)->vmdplugin, fr))
{
gmx_fatal(FARGS, "Not supported in read_first_frame: %s", fn);
}
#else
gmx_fatal(FARGS, "Not supported in read_first_frame: %s. Please make sure that the file is a trajectory.\n"
"GROMACS is not compiled with plug-in support. Thus it cannot read non-GROMACS trajectory formats using the VMD plug-ins.\n"
"Please compile with plug-in support if you want to read non-GROMACS trajectory formats.\n", fn);
#endif
break;
}
(*status)->tf = fr->time;
/* Return FALSE if we read a frame that's past the set ending time. */
if (!bFirst && (!(flags & TRX_DONT_SKIP) && check_times(fr->time) > 0))
{
(*status)->t0 = fr->time;
return FALSE;
}
if (bFirst ||
(!(flags & TRX_DONT_SKIP) && check_times(fr->time) < 0))
{
/* Read a frame when no frame was read or the first was skipped */
if (!read_next_frame(oenv, *status, fr))
{
return FALSE;
}
}
(*status)->t0 = fr->time;
/* We need the number of atoms for random-access XTC searching, even when
* we don't have access to the actual frame data.
*/
(*status)->natoms = fr->natoms;
return (fr->natoms > 0);
}
void close_xtc(int fp)
{
gmx_fio_close(fp);
}
