int read_next_xtc(int fp,
int natoms,int *step,real *time,
matrix box,rvec *x,real *prec,bool *bOK)
{
int magic;
int n;
XDR *xd;
*bOK=TRUE;
xd = gmx_fio_getxdr(fp);
/* read header */
if (!xtc_header(xd,&magic,&n,step,time,TRUE,bOK))
return 0;
/* Check magic number */
check_xtc_magic(magic);
if (n > natoms) {
gmx_fatal(FARGS, "Frame contains more atoms (%d) than expected (%d)",
n, natoms);
}
*bOK=xtc_coord(xd,&natoms,box,x,prec,TRUE);
return *bOK;
}
int read_next_xtc(t_fileio* fio,
int natoms, int64_t *step, real *time,
matrix box, rvec *x, real *prec, gmx_bool *bOK)
{
int magic;
int n;
XDR *xd;
*bOK = TRUE;
xd = gmx_fio_getxdr(fio);
/* read header */
if (!xtc_header(xd, &magic, &n, step, time, TRUE, bOK))
{
return 0;
}
/* Check magic number */
check_xtc_magic(magic);
if (n > natoms)
{
gmx_fatal(FARGS, "Frame contains more atoms (%d) than expected (%d)",
n, natoms);
}
*bOK = (xtc_coord(xd, &natoms, box, x, prec, TRUE) != 0);
return static_cast<int>(*bOK);
}
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 read_xtc_natoms(char *fn,int *natoms)
{
XDRFILE *xd;
int step,result;
float time;
xd = xdrfile_open(fn,"r");
if (NULL == xd)
return exdrFILENOTFOUND;
result = xtc_header(xd,natoms,&step,&time,TRUE);
xdrfile_close(xd);
return result;
}
int write_xtc(XDRFILE *xd,
int natoms,int step,float time,
matrix box,rvec *x,float prec)
/* Write a frame to xtc file */
{
int result;
if ((result = xtc_header(xd,&natoms,&step,&time,FALSE)) != exdrOK)
return result;
if ((result = xtc_coord(xd,&natoms,box,x,&prec,0)) != exdrOK)
return result;
return exdrOK;
}
int read_xtc(XDRFILE *xd,
int natoms,int *step,float *time,
matrix box,rvec *x,float *prec)
/* Read subsequent frames */
{
int result;
if ((result = xtc_header(xd,&natoms,step,time,TRUE)) != exdrOK)
return result;
if ((result = xtc_coord(xd,&natoms,box,x,prec,1)) != exdrOK)
return result;
return exdrOK;
}
int read_first_xtc(int fp,int *natoms,int *step,real *time,
matrix box,rvec **x,real *prec,bool *bOK)
{
int magic;
XDR *xd;
*bOK=TRUE;
xd = gmx_fio_getxdr(fp);
/* read header and malloc x */
if ( !xtc_header(xd,&magic,natoms,step,time,TRUE,bOK))
return 0;
/* Check magic number */
check_xtc_magic(magic);
snew(*x,*natoms);
*bOK=xtc_coord(xd,natoms,box,*x,prec,TRUE);
return *bOK;
}
int read_first_xtc(t_fileio *fio, int *natoms, int64_t *step, real *time,
matrix box, rvec **x, real *prec, gmx_bool *bOK)
{
int magic;
XDR *xd;
*bOK = TRUE;
xd = gmx_fio_getxdr(fio);
/* read header and malloc x */
if (!xtc_header(xd, &magic, natoms, step, time, TRUE, bOK))
{
return 0;
}
/* Check magic number */
check_xtc_magic(magic);
snew(*x, *natoms);
*bOK = (xtc_coord(xd, natoms, box, *x, prec, TRUE) != 0);
return static_cast<int>(*bOK);
}
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 */
}
int read_xtc_numframes(char *fn, int *numframes, int64_t **offsets)
{
XDRFILE *xd;
int framebytes, natoms, step;
float time;
int64_t filesize;
if ((xd = xdrfile_open(fn,"r"))==NULL)
return exdrFILENOTFOUND;
if (xtc_header(xd,&natoms,&step,&time,TRUE) != exdrOK)
{
xdrfile_close(xd);
return exdrHEADER;
}
if (xdr_seek(xd, 0L, SEEK_END) != exdrOK)
{
xdrfile_close(xd);
return exdrNR;
}
filesize = xdr_tell(xd);
/* Case of fewer than 10 atoms. Framesize known. */
if (natoms < 10)
{
int i;
xdrfile_close(xd);
framebytes = XTC_SHORTHEADER_SIZE + XTC_SHORT_BYTESPERATOM*natoms;
*numframes = filesize/framebytes; /* Should we complain if framesize doesn't divide filesize? */
/* Allocate memory for the frame index array */
if ((*offsets=(int64_t *)malloc(sizeof(int64_t)*(*numframes)))==NULL)
return exdrNOMEM;
for (i=0; i<*numframes; i++)
{
(*offsets)[i] = i*framebytes;
}
return exdrOK;
}
else /* No easy way out. We must iterate. */
{
int est_nframes;
/* Estimation of number of frames, with 20% allowance for error. */
if (xdr_seek(xd, (int64_t) XTC_HEADER_SIZE, SEEK_SET) != exdrOK)
{
xdrfile_close(xd);
return exdrNR;
}
if (xdrfile_read_int(&framebytes,1,xd) == 0)
{
xdrfile_close(xd);
return exdrENDOFFILE;
}
framebytes = (framebytes + 3) & ~0x03; //Rounding to the next 32-bit boundary
est_nframes = (int) (filesize/((int64_t) (framebytes+XTC_HEADER_SIZE)) + 1); // add one because it'd be easy to underestimate low frame numbers.
est_nframes += est_nframes/5;
/* Allocate memory for the frame index array */
if ((*offsets=(int64_t *)malloc(sizeof(int64_t)*est_nframes))==NULL)
{
xdrfile_close(xd);
return exdrNOMEM;
}
(*offsets)[0] = 0L;
*numframes = 1;
while (1)
{
if (xdr_seek(xd, (int64_t) (framebytes+XTC_HEADER_SIZE), SEEK_CUR) != exdrOK) {
free(*offsets);
xdrfile_close(xd);
return exdrNR;
}
if (xdrfile_read_int(&framebytes,1,xd) == 0)
break;
/* Read was successful; this is another frame */
/* Check if we need to enlarge array */
if (*numframes == est_nframes){
est_nframes += est_nframes/5 + 1; // Increase in 20% stretches
if ((*offsets = realloc(*offsets, sizeof(int64_t)*est_nframes))==NULL)
{
free(*offsets);
xdrfile_close(xd);
return exdrNOMEM;
}
}
(*offsets)[*numframes] = xdr_tell(xd) - 4L - (int64_t) (XTC_HEADER_SIZE); //Account for the header and the nbytes bytes we read.
(*numframes)++;
framebytes = (framebytes + 3) & ~0x03; //Rounding to the next 32-bit boundary
}
xdrfile_close(xd);
return exdrOK;
}
}