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;
}
float trx_get_time_of_final_frame(t_trxstatus *status)
{
t_fileio *stfio = trx_get_fileio(status);
int filetype = gmx_fio_getftp(stfio);
int bOK;
float lasttime = -1;
if (filetype == efXTC)
{
lasttime =
xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio),
gmx_fio_getxdr(stfio),
status->natoms, &bOK);
if (!bOK)
{
gmx_fatal(FARGS, "Error reading last frame. Maybe seek not supported." );
}
}
else if (filetype == efTNG)
{
tng_trajectory_t tng = status->tng;
if (!tng)
{
gmx_fatal(FARGS, "Error opening TNG file.");
}
lasttime = gmx_tng_get_time_of_final_frame(tng);
}
else
{
gmx_incons("Only supported for TNG and XTC");
}
return lasttime;
}
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;
}
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 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 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 */
}
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);
}
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 gmx_trjcat(int argc, char *argv[])
{
const char *desc[] =
{
"[THISMODULE] concatenates several input trajectory files in sorted order. ",
"In case of double time frames the one in the later file is used. ",
"By specifying [TT]-settime[tt] you will be asked for the start time ",
"of each file. The input files are taken from the command line, ",
"such that a command like [TT]gmx trjcat -f *.trr -o fixed.trr[tt] should do ",
"the trick. Using [TT]-cat[tt], you can simply paste several files ",
"together without removal of frames with identical time stamps.[PAR]",
"One important option is inferred when the output file is amongst the",
"input files. In that case that particular file will be appended to",
"which implies you do not need to store double the amount of data.",
"Obviously the file to append to has to be the one with lowest starting",
"time since one can only append at the end of a file.[PAR]",
"If the [TT]-demux[tt] option is given, the N trajectories that are",
"read, are written in another order as specified in the [TT].xvg[tt] file.",
"The [TT].xvg[tt] file should contain something like:[PAR]",
"[TT]0 0 1 2 3 4 5[BR]",
"2 1 0 2 3 5 4[tt][BR]",
"Where the first number is the time, and subsequent numbers point to",
"trajectory indices.",
"The frames corresponding to the numbers present at the first line",
"are collected into the output trajectory. If the number of frames in",
"the trajectory does not match that in the [TT].xvg[tt] file then the program",
"tries to be smart. Beware."
};
static gmx_bool bVels = TRUE;
static int prec = 3;
static gmx_bool bCat = FALSE;
static gmx_bool bSort = TRUE;
static gmx_bool bKeepLast = FALSE;
static gmx_bool bKeepLastAppend = FALSE;
static gmx_bool bOverwrite = FALSE;
static gmx_bool bSetTime = FALSE;
static gmx_bool bDeMux;
static real begin = -1;
static real end = -1;
static real dt = 0;
t_pargs
pa[] =
{
{ "-b", FALSE, etTIME,
{ &begin }, "First time to use (%t)" },
{ "-e", FALSE, etTIME,
{ &end }, "Last time to use (%t)" },
{ "-dt", FALSE, etTIME,
{ &dt }, "Only write frame when t MOD dt = first time (%t)" },
{ "-prec", FALSE, etINT,
{ &prec }, "Precision for [TT].xtc[tt] and [TT].gro[tt] writing in number of decimal places" },
{ "-vel", FALSE, etBOOL,
{ &bVels }, "Read and write velocities if possible" },
{ "-settime", FALSE, etBOOL,
{ &bSetTime }, "Change starting time interactively" },
{ "-sort", FALSE, etBOOL,
{ &bSort }, "Sort trajectory files (not frames)" },
{ "-keeplast", FALSE, etBOOL,
{ &bKeepLast }, "Keep overlapping frames at end of trajectory" },
{ "-overwrite", FALSE, etBOOL,
{ &bOverwrite }, "Overwrite overlapping frames during appending" },
{ "-cat", FALSE, etBOOL,
{ &bCat }, "Do not discard double time frames" }
};
#define npargs asize(pa)
int ftpin, i, frame, frame_out, step = 0, trjout = 0;
t_trxstatus *status;
rvec *x, *v;
real xtcpr, t_corr;
t_trxframe fr, frout;
char **fnms, **fnms_out, *in_file, *out_file;
int n_append;
t_trxstatus *trxout = NULL;
gmx_bool bNewFile, bIndex, bWrite;
int earliersteps, nfile_in, nfile_out, *cont_type, last_ok_step;
real *readtime, *timest, *settime;
real first_time = 0, lasttime = NOTSET, last_ok_t = -1, timestep;
real last_frame_time, searchtime;
int isize, j;
atom_id *index = NULL, imax;
char *grpname;
real **val = NULL, *t = NULL, dt_remd;
int n, nset;
gmx_bool bOK;
gmx_off_t fpos;
output_env_t oenv;
t_filenm fnm[] =
{
{ efTRX, "-f", NULL, ffRDMULT },
{ efTRO, "-o", NULL, ffWRMULT },
{ efNDX, "-n", "index", ffOPTRD },
{ efXVG, "-demux", "remd", ffOPTRD }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_BE_NICE | PCA_TIME_UNIT, NFILE, fnm,
asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
bIndex = ftp2bSet(efNDX, NFILE, fnm);
bDeMux = ftp2bSet(efXVG, NFILE, fnm);
bSort = bSort && !bDeMux;
imax = NO_ATID;
if (bIndex)
{
printf("Select group for output\n");
rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
/* scan index */
imax = index[0];
for (i = 1; i < isize; i++)
{
imax = max(imax, index[i]);
}
}
if (bDeMux)
{
nset = 0;
dt_remd = 0;
val = read_xvg_time(opt2fn("-demux", NFILE, fnm), TRUE,
opt2parg_bSet("-b", npargs, pa), begin,
opt2parg_bSet("-e", npargs, pa), end, 1, &nset, &n,
&dt_remd, &t);
printf("Read %d sets of %d points, dt = %g\n\n", nset, n, dt_remd);
if (debug)
{
fprintf(debug, "Dump of replica_index.xvg\n");
for (i = 0; (i < n); i++)
{
fprintf(debug, "%10g", t[i]);
for (j = 0; (j < nset); j++)
{
fprintf(debug, " %3d", gmx_nint(val[j][i]));
}
fprintf(debug, "\n");
}
}
}
/* prec is in nr of decimal places, xtcprec is a multiplication factor: */
xtcpr = 1;
for (i = 0; i < prec; i++)
{
xtcpr *= 10;
}
nfile_in = opt2fns(&fnms, "-f", NFILE, fnm);
if (!nfile_in)
{
gmx_fatal(FARGS, "No input files!" );
}
if (bDeMux && (nfile_in != nset))
{
gmx_fatal(FARGS, "You have specified %d files and %d entries in the demux table", nfile_in, nset);
}
nfile_out = opt2fns(&fnms_out, "-o", NFILE, fnm);
if (!nfile_out)
{
gmx_fatal(FARGS, "No output files!");
}
if ((nfile_out > 1) && !bDeMux)
{
gmx_fatal(FARGS, "Don't know what to do with more than 1 output file if not demultiplexing");
}
else if (bDeMux && (nfile_out != nset) && (nfile_out != 1))
{
gmx_fatal(FARGS, "Number of output files should be 1 or %d (#input files), not %d", nset, nfile_out);
}
if (bDeMux)
{
if (nfile_out != nset)
{
char *buf = strdup(fnms_out[0]);
snew(fnms_out, nset);
for (i = 0; (i < nset); i++)
{
snew(fnms_out[i], strlen(buf)+32);
sprintf(fnms_out[i], "%d_%s", i, buf);
}
sfree(buf);
}
do_demux(nfile_in, fnms, fnms_out, n, val, t, dt_remd, isize, index, dt, oenv);
}
else
{
snew(readtime, nfile_in+1);
snew(timest, nfile_in+1);
scan_trj_files(fnms, nfile_in, readtime, timest, imax, oenv);
snew(settime, nfile_in+1);
snew(cont_type, nfile_in+1);
edit_files(fnms, nfile_in, readtime, timest, settime, cont_type, bSetTime, bSort,
oenv);
/* Check whether the output file is amongst the input files
* This has to be done after sorting etc.
*/
out_file = fnms_out[0];
n_append = -1;
for (i = 0; ((i < nfile_in) && (n_append == -1)); i++)
{
if (strcmp(fnms[i], out_file) == 0)
{
n_append = i;
}
}
if (n_append == 0)
{
fprintf(stderr, "Will append to %s rather than creating a new file\n",
out_file);
}
else if (n_append != -1)
{
gmx_fatal(FARGS, "Can only append to the first file which is %s (not %s)",
fnms[0], out_file);
}
earliersteps = 0;
/* Not checking input format, could be dangerous :-) */
/* Not checking output format, equally dangerous :-) */
frame = -1;
frame_out = -1;
/* the default is not to change the time at all,
* but this is overridden by the edit_files routine
*/
t_corr = 0;
if (n_append == -1)
{
trxout = open_trx(out_file, "w");
memset(&frout, 0, sizeof(frout));
}
else
{
t_fileio *stfio;
if (!read_first_frame(oenv, &status, out_file, &fr, FLAGS))
{
gmx_fatal(FARGS, "Reading first frame from %s", out_file);
}
stfio = trx_get_fileio(status);
if (!bKeepLast && !bOverwrite)
{
fprintf(stderr, "\n\nWARNING: Appending without -overwrite implies -keeplast "
"between the first two files. \n"
"If the trajectories have an overlap and have not been written binary \n"
"reproducible this will produce an incorrect trajectory!\n\n");
/* Fails if last frame is incomplete
* We can't do anything about it without overwriting
* */
if (gmx_fio_getftp(stfio) == efXTC)
{
lasttime =
xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio),
gmx_fio_getxdr(stfio),
fr.natoms, &bOK);
fr.time = lasttime;
if (!bOK)
{
gmx_fatal(FARGS, "Error reading last frame. Maybe seek not supported." );
}
}
else
{
while (read_next_frame(oenv, status, &fr))
{
;
}
lasttime = fr.time;
}
bKeepLastAppend = TRUE;
close_trj(status);
trxout = open_trx(out_file, "a");
}
else if (bOverwrite)
{
if (gmx_fio_getftp(stfio) != efXTC)
{
gmx_fatal(FARGS, "Overwrite only supported for XTC." );
}
last_frame_time =
xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio),
gmx_fio_getxdr(stfio),
fr.natoms, &bOK);
if (!bOK)
{
gmx_fatal(FARGS, "Error reading last frame. Maybe seek not supported." );
}
/* xtc_seek_time broken for trajectories containing only 1 or 2 frames
* or when seek time = 0 */
if (nfile_in > 1 && settime[1] < last_frame_time+timest[0]*0.5)
{
/* Jump to one time-frame before the start of next
* trajectory file */
searchtime = settime[1]-timest[0]*1.25;
}
else
{
searchtime = last_frame_time;
}
if (xtc_seek_time(stfio, searchtime, fr.natoms, TRUE))
{
gmx_fatal(FARGS, "Error seeking to append position.");
}
read_next_frame(oenv, status, &fr);
if (fabs(searchtime - fr.time) > timest[0]*0.5)
{
gmx_fatal(FARGS, "Error seeking: attempted to seek to %f but got %f.",
searchtime, fr.time);
}
lasttime = fr.time;
fpos = gmx_fio_ftell(stfio);
close_trj(status);
trxout = open_trx(out_file, "r+");
if (gmx_fio_seek(trx_get_fileio(trxout), fpos))
{
gmx_fatal(FARGS, "Error seeking to append position.");
}
}
printf("\n Will append after %f \n", lasttime);
frout = fr;
}
/* Lets stitch up some files */
timestep = timest[0];
for (i = n_append+1; (i < nfile_in); i++)
{
/* Open next file */
/* set the next time from the last frame in previous file */
if (i > 0)
{
if (frame_out >= 0)
{
if (cont_type[i] == TIME_CONTINUE)
{
begin = frout.time;
begin += 0.5*timestep;
settime[i] = frout.time;
cont_type[i] = TIME_EXPLICIT;
}
else if (cont_type[i] == TIME_LAST)
{
begin = frout.time;
begin += 0.5*timestep;
}
/* Or, if the time in the next part should be changed by the
* same amount, start at half a timestep from the last time
* so we dont repeat frames.
*/
/* I don't understand the comment above, but for all the cases
* I tried the code seems to work properly. B. Hess 2008-4-2.
*/
}
/* Or, if time is set explicitly, we check for overlap/gap */
if (cont_type[i] == TIME_EXPLICIT)
{
if ( ( i < nfile_in ) &&
( frout.time < settime[i]-1.5*timestep ) )
{
fprintf(stderr, "WARNING: Frames around t=%f %s have a different "
"spacing than the rest,\n"
"might be a gap or overlap that couldn't be corrected "
"automatically.\n", output_env_conv_time(oenv, frout.time),
output_env_get_time_unit(oenv));
}
}
}
/* if we don't have a timestep in the current file, use the old one */
if (timest[i] != 0)
{
timestep = timest[i];
}
read_first_frame(oenv, &status, fnms[i], &fr, FLAGS);
if (!fr.bTime)
{
fr.time = 0;
fprintf(stderr, "\nWARNING: Couldn't find a time in the frame.\n");
}
if (cont_type[i] == TIME_EXPLICIT)
{
t_corr = settime[i]-fr.time;
}
/* t_corr is the amount we want to change the time.
* If the user has chosen not to change the time for
* this part of the trajectory t_corr remains at
* the value it had in the last part, changing this
* by the same amount.
* If no value was given for the first trajectory part
* we let the time start at zero, see the edit_files routine.
*/
bNewFile = TRUE;
printf("\n");
if (lasttime != NOTSET)
{
printf("lasttime %g\n", lasttime);
}
do
{
/* copy the input frame to the output frame */
frout = fr;
/* set the new time by adding the correct calculated above */
frout.time += t_corr;
/* quit if we have reached the end of what should be written */
if ((end > 0) && (frout.time > end+GMX_REAL_EPS))
{
i = nfile_in;
break;
}
/* determine if we should write this frame (dt is handled elsewhere) */
if (bCat) /* write all frames of all files */
{
bWrite = TRUE;
}
else if (bKeepLast || (bKeepLastAppend && i == 1))
/* write till last frame of this traj
and skip first frame(s) of next traj */
{
bWrite = ( frout.time > lasttime+0.5*timestep );
}
else /* write till first frame of next traj */
{
bWrite = ( frout.time < settime[i+1]-0.5*timestep );
}
if (bWrite && (frout.time >= begin) )
{
frame++;
if (frame_out == -1)
{
first_time = frout.time;
}
lasttime = frout.time;
if (dt == 0 || bRmod(frout.time, first_time, dt))
{
frame_out++;
last_ok_t = frout.time;
if (bNewFile)
{
fprintf(stderr, "\nContinue writing frames from %s t=%g %s, "
"frame=%d \n",
fnms[i], output_env_conv_time(oenv, frout.time), output_env_get_time_unit(oenv),
frame);
bNewFile = FALSE;
}
if (bIndex)
{
write_trxframe_indexed(trxout, &frout, isize, index,
NULL);
}
else
{
write_trxframe(trxout, &frout, NULL);
}
if ( ((frame % 10) == 0) || (frame < 10) )
{
fprintf(stderr, " -> frame %6d time %8.3f %s \r",
frame_out, output_env_conv_time(oenv, frout.time), output_env_get_time_unit(oenv));
}
}
}
}
while (read_next_frame(oenv, status, &fr));
close_trj(status);
earliersteps += step;
}
if (trxout)
{
close_trx(trxout);
}
fprintf(stderr, "\nLast frame written was %d, time %f %s\n",
frame, output_env_conv_time(oenv, last_ok_t), output_env_get_time_unit(oenv));
}
return 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 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);
}
